15-63020496-T-C

Variant names:

• chr15-63020496-T-C
• rs7179658

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 0.649 in 152,150 control chromosomes in the GnomAD database, including 33,287 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 0.65 (33287 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 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: 0.649 AC: 98706 AN: 152032 Hom.: 33276 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.649 AC: 98757 AN: 152150 Hom.: 33287 Cov.: 33 AF XY: 0.642 AC XY: 47806 AN XY: 74408

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.684

Alfa AF: 0.681 Hom.: 4198

Bravo AF: 0.647

Asia WGS AF: 0.350 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7179658; hg19: chr15-63312695;