rs7916940

Variant names:

• chr10-121436796-A-G
• rs7916940

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 0.645 in 151,986 control chromosomes in the GnomAD database, including 32,115 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 0.64 (32115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.36
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 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: 0.645 AC: 97961 AN: 151868 Hom.: 32090 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.645 AC: 98030 AN: 151986 Hom.: 32115 Cov.: 32 AF XY: 0.643 AC XY: 47762 AN XY: 74272

African (AFR) AF: 0.552 AC: 22849 AN: 41424

American (AMR) AF: 0.584 AC: 8917 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2837 AN: 5156

South Asian (SAS) AF: 0.658 AC: 3158 AN: 4802

European-Finnish (FIN) AF: 0.721 AC: 7623 AN: 10574

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.711 AC: 48357 AN: 67972

Other (OTH) AF: 0.642 AC: 1354 AN: 2108

Alfa AF: 0.686 Hom.: 18208

Bravo AF: 0.628

Asia WGS AF: 0.621 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.60
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs7916940; hg19: chr10-123196310;