chr6-32708012-G-A

Variant names:

• chr6-32708012-G-A
• rs9275535

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 0.589 in 151,764 control chromosomes in the GnomAD database, including 26,733 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 0.59 (26733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.590 AC: 89402 AN: 151646 Hom.: 26726 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.589 AC: 89457 AN: 151764 Hom.: 26733 Cov.: 31 AF XY: 0.590 AC XY: 43738 AN XY: 74160

African (AFR) AF: 0.561 AC: 23221 AN: 41386

American (AMR) AF: 0.643 AC: 9817 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2604 AN: 3458

East Asian (EAS) AF: 0.730 AC: 3775 AN: 5172

South Asian (SAS) AF: 0.667 AC: 3210 AN: 4810

European-Finnish (FIN) AF: 0.543 AC: 5715 AN: 10526

Middle Eastern (MID) AF: 0.670 AC: 193 AN: 288

European-Non Finnish (NFE) AF: 0.574 AC: 38915 AN: 67840

Other (OTH) AF: 0.640 AC: 1349 AN: 2108

Alfa AF: 0.574 Hom.: 3183

Bravo AF: 0.599

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.3
DANN	Benign	0.53
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9275535; hg19: chr6-32675789;