10-128493474-A-G

Variant names:

• chr10-128493474-A-G
• rs7893667

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 0.62 in 152,064 control chromosomes in the GnomAD database, including 30,290 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 0.62 (30290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 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: 0.620 AC: 94277 AN: 151946 Hom.: 30286 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.620 AC: 94305 AN: 152064 Hom.: 30290 Cov.: 32 AF XY: 0.621 AC XY: 46167 AN XY: 74344

African (AFR) AF: 0.460 AC: 19068 AN: 41452

American (AMR) AF: 0.706 AC: 10795 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1994 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2591 AN: 5158

South Asian (SAS) AF: 0.684 AC: 3294 AN: 4816

European-Finnish (FIN) AF: 0.674 AC: 7123 AN: 10576

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47267 AN: 67982

Other (OTH) AF: 0.612 AC: 1292 AN: 2112

Alfa AF: 0.677 Hom.: 58169

Bravo AF: 0.616

Asia WGS AF: 0.586 AC: 2037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.59
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs7893667; hg19: chr10-130291738;