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SNV:21-31154350-T-A (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	Pass	Pass	Discrepant frequencies
Allele Count	28741	2134	30875
Allele Number	1461866	151822	1613688
Allele Frequency	0.01966	0.01406	0.01913
Grpmax Filtering AF (95% confidence)	0.02221 European (non-Finnish)	0.02002 European (non-Finnish)	0.02213 European (non-Finnish)
Number of homozygotes	364	26	390

External Resources

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Genetic Ancestry Group Frequencies

gnomAD
HGDP
1KG
Local Ancestry


	47	912	1	0.05154
	1738	63936	28	0.02718
	26381	1179932	323	0.02236
	885	62500	7	0.01416
	1053	91036	25	0.01157
	52	6062	1	0.008578
	385	59986	3	0.006418
	268	74876	1	0.003579
	64	29606	1	0.002162
	2	44842	0	0.00004460
XX	15630	812334	188	0.01924
XY	15245	801354	202	0.01902
Total	30875	1613688	390	0.01913

Include:ExomesGenomes


	6	362	0.01657
	2	300	0.006667
	0	198	0.000
	0	436	0.000
	0	280	0.000
	0	100	0.000
	0	28	0.000
XX	2	586	0.003413
XY	6	1118	0.005367
Total	8	1704	0.004695


	18	1022	0.01761
	8	990	0.008081
	4	680	0.005882
	2	1286	0.001555
	0	990	0.000
XX	12	2476	0.004847
XY	20	2492	0.008026
Total	32	4968	0.006441


	Overall	157	40288	0.003897
European	155	7965	0.01946
African	2	32323	0.00006188
Total	157	40288	0.003897

Related Variants

Other Alternate Alleles

This variant is multiallelic. Other alternate alleles are:

21-31154350-T-C

Liftover

The following GRCh37 variant lifts over to this variant:

21-32526668-T-A
View variant in gnomAD v2.1.1

Nearby Variants

View variants located within 20 bases of this variant.

Variant Effect Predictor

This variant falls on 4 transcripts in 1 gene.

Note The gene symbols shown below are provided by VEP and may differ from the symbol shown on gene pages.

missense
1. TIAM1
  1. ENST00000541036.6
    MANE Select transcript for TIAM1
    HGVSp
    p.Asp1023Val
    Domains
    mobidb (MobiDB_lite)
    PTHR46001 (PANTHER)
  2. ENST00000286827.7
    HGVSp
    p.Asp1023Val
    Domains
    mobidb (MobiDB_lite)
    PTHR46001 (PANTHER)
  3. ENST00000455508.2
    HGVSp
    p.Asp963Val
    Domains
    mobidb (MobiDB_lite)
    PTHR46001 (PANTHER)

In Silico Predictors

CADD: 22.9
REVEL: 0.0960
SpliceAI: 0.0300
Pangolin: -0.460
phyloP: 6.30
PolyPhen (max): 0.0100

Note For more detailed and up to date SpliceAI and Pangolin predictions, please visit our SpliceAI Lookup browser

Genomic Constraint of Surrounding 1kb Region

Genomic constraint values displayed are for the region: 21-31154000-31155000

Expected	Observed	Constraint
193.2	156	Z = 2.68 o/e = 0.81

ClinVar

ClinVar Variation ID: 3038397
Conditions: TIAM1-related disorder
Germline classification: Benign
Review status: no assertion criteria provided (0 stars)
Last evaluated: July 9, 2024

or find more information on the ClinVar website. Data displayed here is from ClinVar's February 1, 2025 release.

Age Distribution

Exome
Genome

Variant carriers
All individuals

Include heterozygous variant carriersInclude homozygous variant carriersCompare to all individuals

Sequencing types:

Genotype Quality Metrics

Genotype quality
Depth
Allele balance for heterozygotes

Exome
Genome

Variant carriers
All individuals

Compare to all individualsSequencing types:

Site Quality Metrics

Metric distribution
All metric values

Exome
Genome

Metric: Sequencing types:

Value: 3.064e+7 (exome samples), 1.935e+6 (genome samples)

Site quality approximation for all variants with 0.01 <= AF < 0.02.

Note: These are site-level quality metrics, they may be unpredictable for multi-allelic sites.

Metric	Exome samples	Genome samples
SiteQuality	3.064e+7	1.935e+6
inbreeding_coeff	0.006	0.011
AS_FS	0	0
AS_MQ	60	59.998
AS_MQRankSum	0	-0.047
AS_pab_max	1	1
AS_QUALapprox	3.064e+7	1.935e+6
AS_QD	12.278	13.604
AS_ReadPosRankSum	-0.015	0.293
AS_SOR	0.678	0.701
AS_VarDP	6.3972	5.1531
AS_VQSLOD	9.274	21.776

Read Data

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