6-32714887-C-T

Variant names:

• chr6-32714887-C-T
• rs9275601

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 0.435 in 151,998 control chromosomes in the GnomAD database, including 14,632 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 0.43 (14632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.483 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: 0.435 AC: 66010 AN: 151880 Hom.: 14607 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.435 AC: 66092 AN: 151998 Hom.: 14632 Cov.: 32 AF XY: 0.429 AC XY: 31853 AN XY: 74326

African (AFR) AF: 0.446 AC: 18456 AN: 41422

American (AMR) AF: 0.436 AC: 6665 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2009 AN: 3472

East Asian (EAS) AF: 0.499 AC: 2582 AN: 5172

South Asian (SAS) AF: 0.420 AC: 2023 AN: 4812

European-Finnish (FIN) AF: 0.322 AC: 3406 AN: 10580

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29351 AN: 67952

Other (OTH) AF: 0.492 AC: 1037 AN: 2108

Alfa AF: 0.445 Hom.: 38661

Bravo AF: 0.446

Asia WGS AF: 0.458 AC: 1592 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	0.29
DANN	Benign	0.54
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs9275601; hg19: chr6-32682664;