rs6495126

Positions:

• chr15-74882685-A-G

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 0.671 in 151,966 control chromosomes in the GnomAD database, including 34,514 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 0.67 (34514 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 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: 0.671 AC: 101941 AN: 151846 Hom.: 34475 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.671 AC: 102028 AN: 151966 Hom.: 34514 Cov.: 31 AF XY: 0.669 AC XY: 49699 AN XY: 74274

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.674

Alfa AF: 0.684 Hom.: 48335

Bravo AF: 0.681

Asia WGS AF: 0.798 AC: 2777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6495126; hg19: chr15-75175026; COSMIC: COSV53421904;