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SNV:2-216414821-C-T (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	Pass	Pass	Discrepant frequencies
Allele Count	28	14	42
Allele Number	1461894	152310	1614204
Allele Frequency	0.00001915	0.00009192	0.00002602
Grpmax Filtering AF (95% confidence)	0.0003959 East Asian	0.001632 East Asian	0.0006145 East Asian
Number of homozygotes	0	0	0

External Resources

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Genetic Ancestry Group Frequencies

gnomAD
HGDP
1KG
Local Ancestry


	37	44884	0.0008243
	2	62512	0.00003199
	1	60028	0.00001666
	2	1180046	0.000001695
	0	75030	0.000
	0	29608	0.000
	0	64040	0.000
	0	6062	0.000
	0	912	0.000
	0	91082	0.000
XX	23	812486	0.00002831
XY	19	801718	0.00002370
Total	42	1614204	0.00002602

Include:ExomesGenomes


	1	440	0.002273
	0	198	0.000
	0	302	0.000
	0	280	0.000
	0	100	0.000
	0	362	0.000
	0	28	0.000
XX	1	588	0.001701
XY	0	1122	0.000
Total	1	1710	0.0005848


	1	990	0.001010
	0	1286	0.000
	0	680	0.000
	0	1022	0.000
	0	990	0.000
XX	0	2476	0.000
XY	1	2492	0.0004013
Total	1	4968	0.0002013

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

2-217279544-C-T
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 5 transcripts in 1 gene.

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

synonymous
1. SMARCAL1
  1. ENST00000357276.9
    MANE Select transcript for SMARCAL1
    HGVSp
    p.Gly39Gly
    Domains
    mobidb (MobiDB_lite)
    PTHR45766 (PANTHER)
  2. ENST00000358207.9
    HGVSp
    p.Gly39Gly
    Domains
    mobidb (MobiDB_lite)
    PTHR45766 (PANTHER)
  3. ENST00000430374.5
    HGVSp
    p.Gly39Gly
    Domains
    mobidb (MobiDB_lite)

In Silico Predictors

CADD: 8.57
SpliceAI: 0.820
Pangolin: 0.390
phyloP: 0.894

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: 2-216414000-216415000

Expected	Observed	Constraint
84	82	Z = 0.22 o/e = 0.98

ClinVar

ClinVar Variation ID: 791007
Conditions: Schimke immuno-osseous dysplasia
Germline classification: Likely benign
Review status: criteria provided, single submitter (1 star)
Last evaluated: January 29, 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: 9.692e+4 (exome samples), 6.491e+3 (genome samples)

Site quality approximation for all variants with 0.00005 <= AF < 0.0001.

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

Metric	Exome samples	Genome samples
SiteQuality	9.692e+4	6.491e+3
inbreeding_coeff	-1.915e-5	-9.186e-5
AS_FS	0	1.731
AS_MQ	59.998	59.968
AS_MQRankSum	0	-0.246
AS_pab_max	1	1
AS_QUALapprox	9.692e+4	6.491e+3
AS_QD	12.408	12.727
AS_ReadPosRankSum	0.123	0.397
AS_SOR	0.727	0.568
AS_VarDP	3.8927	2.7076
AS_VQSLOD	7.724	1.003

Read Data

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