10-131816128-G-A

Variant names:

• chr10-131816128-G-A
• rs7903156

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 0.898 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.973 AC: 40240 AN: 41362

American (AMR) AF: 0.885 AC: 13540 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2838 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5160 AN: 5174

South Asian (SAS) AF: 0.926 AC: 4463 AN: 4822

European-Finnish (FIN) AF: 0.884 AC: 9363 AN: 10592

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58120 AN: 68002

Other (OTH) AF: 0.874 AC: 1845 AN: 2112

Alfa AF: 0.912 Hom.: 17319

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7903156; hg19: chr10-133648464;