6-32768918-A-T

Variant names:

• chr6-32768918-A-T
• rs9276606

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 0.253 in 151,886 control chromosomes in the GnomAD database, including 4,921 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 0.25 (4921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38375 AN: 151772 Hom.: 4923 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.253 AC: 38396 AN: 151886 Hom.: 4921 Cov.: 32 AF XY: 0.250 AC XY: 18529 AN XY: 74222

African (AFR) AF: 0.267 AC: 11042 AN: 41390

American (AMR) AF: 0.238 AC: 3630 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3468

East Asian (EAS) AF: 0.140 AC: 724 AN: 5178

South Asian (SAS) AF: 0.209 AC: 1004 AN: 4812

European-Finnish (FIN) AF: 0.224 AC: 2351 AN: 10506

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18120 AN: 67938

Other (OTH) AF: 0.242 AC: 509 AN: 2104

Alfa AF: 0.118 Hom.: 219

Bravo AF: 0.248

Asia WGS AF: 0.194 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9276606; hg19: chr6-32736695; COSMIC: COSV67207804;