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SNV:9-112299168-G-A (GRCh38)

Dataset

gnomAD v4.1.0

	Exomes	Genomes	Total
Filters	No data	Pass	Not in exomes
Allele Count	-	40410	40410
Allele Number	-	152086	152086
Allele Frequency	-	0.2657	0.2657
Grpmax Filtering AF (95% confidence)	-	0.3914 South Asian	0.3914 South Asian
Number of homozygotes	-	6679	6679

External Resources

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Genetic Ancestry Group Frequencies

gnomAD
HGDP
1KG
Local Ancestry


	4720	10570	1057	0.4465
	1520	3468	337	0.4383
	1958	4818	423	0.4064
	1931	5176	360	0.3731
	5352	15276	967	0.3504
	97	294	14	0.3299
	658	2112	96	0.3116
	21050	67952	3281	0.3098
	261	912	36	0.2862
	2863	41508	108	0.06897
XX	19960	77750	3165	0.2567
XY	20450	74336	3514	0.2751
Total	40410	152086	6679	0.2657

Include:ExomesGenomes


	53	100	10	0.5300
	13	28	3	0.4643
	165	436	27	0.3784
	124	360	24	0.3444
	100	302	19	0.3311
	86	280	12	0.3071
	2	198	0	0.01010
XX	202	588	40	0.3435
XY	341	1116	55	0.3056
Total	543	1704	95	0.3187

Warning Because of low sample sizes for HGDP populations, allele frequencies may not be representative.


	400	990	86	0.4040
	265	680	49	0.3897
	349	990	63	0.3525
	326	1022	53	0.3190
	28	1286	0	0.02177
XX	693	2476	123	0.2799
XY	675	2492	128	0.2709
Total	1368	4968	251	0.2754


	Overall	2861	40398	0.07082
European	2486	7839	0.3171
African	375	32559	0.01152
Total	2861	40398	0.07082

Related Variants

Liftover

The following GRCh37 variant lifts over to this variant:

9-115061448-G-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 8 transcripts in 1 gene.

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

intron
1. PTBP3
  1. ENST00000374257.6
    MANE Select transcript for PTBP3
    HGVSc
    c.-51-1252C>T
  2. ENST00000210227.4
    HGVSc
    c.61-1252C>T
  3. ENST00000334318.10
    HGVSc
    c.43-1252C>T

In Silico Predictors

CADD: 4.84
SpliceAI: 0.00
Pangolin: 0.00
phyloP: -1.64

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: 9-112299000-112300000

Expected	Observed	Constraint
117.6	109	Z = 0.79 o/e = 0.93

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: 4.306e+7 (genome samples)

Site quality approximation for all variants with 0.2 <= AF < 0.5.

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

Metric	Genome samples
SiteQuality	4.306e+7
inbreeding_coeff	0.089
AS_FS	9.643e-16
AS_MQ	59.997
AS_MQRankSum	-0.044
AS_pab_max	1
AS_QUALapprox	4.306e+7
AS_QD	17.699
AS_ReadPosRankSum	0.353
AS_SOR	0.68
AS_VarDP	6.3861
AS_VQSLOD	21.03

Read Data

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