10-62810651-C-T

Position:

• chr10-62810651-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.0572

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0728 Hom.: 891

Bravo AF: 0.128

Asia WGS AF: 0.218 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1509963; hg19: chr10-64570411;