rs7913531

Variant names:

• chr10-122696517-C-A
• rs7913531

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 0.361 in 152,078 control chromosomes in the GnomAD database, including 10,146 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 0.36 (10146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 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: 0.361 AC: 54809 AN: 151958 Hom.: 10139 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.361 AC: 54836 AN: 152078 Hom.: 10146 Cov.: 32 AF XY: 0.362 AC XY: 26888 AN XY: 74320

African (AFR) AF: 0.308 AC: 12775 AN: 41472

American (AMR) AF: 0.308 AC: 4700 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1959 AN: 5172

South Asian (SAS) AF: 0.472 AC: 2275 AN: 4816

European-Finnish (FIN) AF: 0.410 AC: 4324 AN: 10558

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26231 AN: 67992

Other (OTH) AF: 0.367 AC: 776 AN: 2114

Alfa AF: 0.377 Hom.: 41429

Bravo AF: 0.348

Asia WGS AF: 0.421 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.70
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7913531; hg19: chr10-124456033;