rs2647087

Variant names:

• chr6-32713272-A-C
• rs2647087

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.297 in 152,122 control chromosomes in the GnomAD database, including 7,172 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 0.30 (7172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 56 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 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: 0.297 AC: 45134 AN: 152004 Hom.: 7174 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.297 AC: 45147 AN: 152122 Hom.: 7172 Cov.: 32 AF XY: 0.293 AC XY: 21785 AN XY: 74358

African (AFR) AF: 0.320 AC: 13257 AN: 41482

American (AMR) AF: 0.322 AC: 4920 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2096 AN: 5168

South Asian (SAS) AF: 0.456 AC: 2200 AN: 4820

European-Finnish (FIN) AF: 0.121 AC: 1282 AN: 10604

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18788 AN: 67976

Other (OTH) AF: 0.364 AC: 768 AN: 2112

Alfa AF: 0.287 Hom.: 24246

Bravo AF: 0.311

Asia WGS AF: 0.456 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.34
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2647087; hg19: chr6-32681049;