15-62926338-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 0.643 in 152,070 control chromosomes in the GnomAD database, including 31,738 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 0.64 (31738 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.643 AC: 97715 AN: 151952 Hom.: 31721 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.643 AC: 97774 AN: 152070 Hom.: 31738 Cov.: 31 AF XY: 0.642 AC XY: 47728 AN XY: 74332

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.690

Alfa AF: 0.583 Hom.: 3332

Bravo AF: 0.646

Asia WGS AF: 0.720 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.5
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs902027; hg19: chr15-63218537;