rs7903156

Variant names:

• chr10-131816128-G-A
• rs7903156

Your query was ambiguous. Multiple possible variants found:

• chr10-131816128-G-A
• chr10-131816128-G-C

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 0.898 in 152,038 control chromosomes in the GnomAD database, including 61,655 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 0.90 (61655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.898 AC: 136487 AN: 151920 Hom.: 61598 Cov.: 32

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.898 AC: 136602 AN: 152038 Hom.: 61655 Cov.: 32 AF XY: 0.901 AC XY: 67008 AN XY: 74334

Gnomad4 AFR AF: 0.973

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.874

Alfa AF: 0.888 Hom.: 10634

Bravo AF: 0.901

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.56
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7903156; hg19: chr10-133648464;