10-36166967-C-A

Variant names:

• chr10-36166967-C-A
• rs315644

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 0.716 in 152,028 control chromosomes in the GnomAD database, including 40,157 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 0.72 (40157 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108726 AN: 151910 Hom.: 40120 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.716 AC: 108816 AN: 152028 Hom.: 40157 Cov.: 31 AF XY: 0.715 AC XY: 53116 AN XY: 74334

African (AFR) AF: 0.525 AC: 21756 AN: 41418

American (AMR) AF: 0.766 AC: 11704 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2427 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4093 AN: 5178

South Asian (SAS) AF: 0.761 AC: 3665 AN: 4814

European-Finnish (FIN) AF: 0.761 AC: 8036 AN: 10562

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54679 AN: 67986

Other (OTH) AF: 0.711 AC: 1498 AN: 2108

Alfa AF: 0.771 Hom.: 75833

Bravo AF: 0.706

Asia WGS AF: 0.765 AC: 2659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.35
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs315644; hg19: chr10-36455895;