10-62977815-T-A

Variant names:

• chr10-62977815-T-A
• rs79965208

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.39 (7097 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 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: 0.389 AC: 38669 AN: 99530 Hom.: 7098 Cov.: 19

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.428

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.388 AC: 38676 AN: 99594 Hom.: 7097 Cov.: 19 AF XY: 0.389 AC XY: 18777 AN XY: 48326

African (AFR) AF: 0.218 AC: 4621 AN: 21232

American (AMR) AF: 0.501 AC: 5437 AN: 10846

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 843 AN: 2218

East Asian (EAS) AF: 0.308 AC: 1182 AN: 3832

South Asian (SAS) AF: 0.492 AC: 1580 AN: 3212

European-Finnish (FIN) AF: 0.333 AC: 2189 AN: 6576

Middle Eastern (MID) AF: 0.421 AC: 75 AN: 178

European-Non Finnish (NFE) AF: 0.443 AC: 21836 AN: 49326

Other (OTH) AF: 0.413 AC: 591 AN: 1432

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs79965208; hg19: chr10-64737575; COSMIC: COSV55986703;