10-62307749-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 0.694 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.695

Alfa AF: 0.698 Hom.: 24461

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3910172; hg19: chr10-64067508;