6-32684540-A-T

Variant names:

• chr6-32684540-A-T
• rs7755224

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 0.256 in 151,116 control chromosomes in the GnomAD database, including 5,348 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 0.26 (5348 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933
• Publications: 38 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38723 AN: 151002 Hom.: 5354 Cov.: 30

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.256 AC: 38732 AN: 151116 Hom.: 5348 Cov.: 30 AF XY: 0.253 AC XY: 18646 AN XY: 73824

African (AFR) AF: 0.260 AC: 10727 AN: 41232

American (AMR) AF: 0.237 AC: 3595 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 998 AN: 3440

East Asian (EAS) AF: 0.433 AC: 2199 AN: 5082

South Asian (SAS) AF: 0.241 AC: 1154 AN: 4794

European-Finnish (FIN) AF: 0.180 AC: 1889 AN: 10492

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17204 AN: 67646

Other (OTH) AF: 0.274 AC: 574 AN: 2098

Alfa AF: 0.00 Hom.: 74

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.1
DANN	Benign	0.50
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs7755224; hg19: chr6-32652317; COSMIC: COSV64604073;