10-62811516-G-A

Variant names:

• chr10-62811516-G-A
• rs2295814

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0556 in 152,304 control chromosomes in the GnomAD database, including 311 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 0.056 (311 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8461 AN: 152186 Hom.: 309 Cov.: 33

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0556 AC: 8471 AN: 152304 Hom.: 311 Cov.: 33 AF XY: 0.0557 AC XY: 4147 AN XY: 74476

African (AFR) AF: 0.0144 AC: 598 AN: 41566

American (AMR) AF: 0.0592 AC: 906 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3472

East Asian (EAS) AF: 0.162 AC: 840 AN: 5186

South Asian (SAS) AF: 0.0630 AC: 304 AN: 4828

European-Finnish (FIN) AF: 0.0627 AC: 665 AN: 10614

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0699 AC: 4756 AN: 68024

Other (OTH) AF: 0.0591 AC: 125 AN: 2114

Alfa AF: 0.0559 Hom.: 51

Bravo AF: 0.0535

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	23
DANN	Benign	0.88
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs2295814; hg19: chr10-64571276;