6-32698961-C-T

Variant names:

• chr6-32698961-C-T
• rs2856725

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 0.641 in 152,008 control chromosomes in the GnomAD database, including 31,574 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 0.64 (31574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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: 0.641 AC: 97290 AN: 151890 Hom.: 31552 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.641 AC: 97363 AN: 152008 Hom.: 31574 Cov.: 32 AF XY: 0.645 AC XY: 47921 AN XY: 74272

African (AFR) AF: 0.626 AC: 25952 AN: 41448

American (AMR) AF: 0.729 AC: 11142 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2657 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4233 AN: 5170

South Asian (SAS) AF: 0.679 AC: 3270 AN: 4814

European-Finnish (FIN) AF: 0.658 AC: 6938 AN: 10542

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40826 AN: 67954

Other (OTH) AF: 0.680 AC: 1438 AN: 2114

Alfa AF: 0.627 Hom.: 29061

Bravo AF: 0.650

Asia WGS AF: 0.767 AC: 2659 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.2
DANN	Benign	0.36
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2856725; hg19: chr6-32666738;