chr15-62105035-G-A

Position:

• chr15-62105035-G-A

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 0.307 in 151,956 control chromosomes in the GnomAD database, including 8,087 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 0.31 (8087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 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: 0.307 AC: 46618 AN: 151838 Hom.: 8058 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.307 AC: 46704 AN: 151956 Hom.: 8087 Cov.: 32 AF XY: 0.309 AC XY: 22922 AN XY: 74244

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.288

Alfa AF: 0.236 Hom.: 8894

Bravo AF: 0.309

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1370176; hg19: chr15-62397234;