10-62307749-C-T

Variant names:

• chr10-62307749-C-T
• rs3910172

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 0.694 in 152,020 control chromosomes in the GnomAD database, including 37,142 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 0.69 (37142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.694 AC: 105443 AN: 151902 Hom.: 37136 Cov.: 32

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.694 AC: 105492 AN: 152020 Hom.: 37142 Cov.: 32 AF XY: 0.699 AC XY: 51895 AN XY: 74292

African (AFR) AF: 0.610 AC: 25261 AN: 41440

American (AMR) AF: 0.749 AC: 11445 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2396 AN: 3472

East Asian (EAS) AF: 0.921 AC: 4753 AN: 5158

South Asian (SAS) AF: 0.533 AC: 2567 AN: 4814

European-Finnish (FIN) AF: 0.808 AC: 8540 AN: 10564

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.710 AC: 48292 AN: 67976

Other (OTH) AF: 0.695 AC: 1470 AN: 2114

Alfa AF: 0.694 Hom.: 42356

Bravo AF: 0.693

Asia WGS AF: 0.715 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.77
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs3910172; hg19: chr10-64067508;