10-62810651-C-T

Variant names:

• chr10-62810651-C-T
• rs1509963

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 0.118 in 151,892 control chromosomes in the GnomAD database, including 1,479 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 0.12 (1479 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17878 AN: 151774 Hom.: 1473 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.118 AC: 17907 AN: 151892 Hom.: 1479 Cov.: 33 AF XY: 0.124 AC XY: 9215 AN XY: 74192

African (AFR) AF: 0.150 AC: 6201 AN: 41422

American (AMR) AF: 0.233 AC: 3552 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5164

South Asian (SAS) AF: 0.177 AC: 851 AN: 4808

European-Finnish (FIN) AF: 0.152 AC: 1592 AN: 10502

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0572 AC: 3887 AN: 67956

Other (OTH) AF: 0.107 AC: 225 AN: 2106

Alfa AF: 0.0829 Hom.: 1688

Bravo AF: 0.128

Asia WGS AF: 0.218 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.70
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs1509963; hg19: chr10-64570411;