6-32792937-G-T

Variant names:

• chr6-32792937-G-T
• rs2157082

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 0.614 in 151,976 control chromosomes in the GnomAD database, including 28,886 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 0.61 (28886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 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: 0.615 AC: 93317 AN: 151858 Hom.: 28871 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.614 AC: 93371 AN: 151976 Hom.: 28886 Cov.: 32 AF XY: 0.620 AC XY: 46031 AN XY: 74290

African (AFR) AF: 0.638 AC: 26444 AN: 41420

American (AMR) AF: 0.577 AC: 8819 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3593 AN: 5154

South Asian (SAS) AF: 0.712 AC: 3431 AN: 4818

European-Finnish (FIN) AF: 0.679 AC: 7167 AN: 10556

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39660 AN: 67962

Other (OTH) AF: 0.613 AC: 1293 AN: 2110

Alfa AF: 0.594 Hom.: 45546

Bravo AF: 0.606

Asia WGS AF: 0.689 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.75
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2157082; hg19: chr6-32760714;