rs10508531

Variant names:

• chr10-17514377-T-G
• rs10508531

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.108 in 152,248 control chromosomes in the GnomAD database, including 1,070 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16389 AN: 152130 Hom.: 1071 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.100

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 16389 AN: 152248 Hom.: 1070 Cov.: 32 AF XY: 0.104 AC XY: 7759 AN XY: 74446

African (AFR) AF: 0.0494 AC: 2053 AN: 41558

American (AMR) AF: 0.0670 AC: 1025 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0995 AC: 345 AN: 3468

East Asian (EAS) AF: 0.0568 AC: 294 AN: 5180

South Asian (SAS) AF: 0.135 AC: 653 AN: 4828

European-Finnish (FIN) AF: 0.134 AC: 1420 AN: 10602

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.151 AC: 10260 AN: 68000

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.137 Hom.: 957

Bravo AF: 0.0999

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		0.038

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10508531; hg19: chr10-17556376;