rs7913531

Variant names:

• chr10-122696517-C-A
• rs7913531

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.367

Alfa AF: 0.384 Hom.: 17310

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7913531; hg19: chr10-124456033;