6-32703471-G-A

Variant names:

• chr6-32703471-G-A
• rs1794275

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 0.21 in 151,358 control chromosomes in the GnomAD database, including 3,595 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 0.21 (3595 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 61 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 (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31763 AN: 151238 Hom.: 3589 Cov.: 30

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.210 AC: 31811 AN: 151358 Hom.: 3595 Cov.: 30 AF XY: 0.216 AC XY: 15953 AN XY: 73852

African (AFR) AF: 0.243 AC: 10026 AN: 41198

American (AMR) AF: 0.231 AC: 3517 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3466

East Asian (EAS) AF: 0.173 AC: 887 AN: 5118

South Asian (SAS) AF: 0.189 AC: 904 AN: 4784

European-Finnish (FIN) AF: 0.330 AC: 3416 AN: 10360

Middle Eastern (MID) AF: 0.155 AC: 45 AN: 290

European-Non Finnish (NFE) AF: 0.173 AC: 11730 AN: 67922

Other (OTH) AF: 0.212 AC: 446 AN: 2102

Alfa AF: 0.180 Hom.: 8699

Bravo AF: 0.205

Asia WGS AF: 0.219 AC: 766 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	1.8
DANN	Benign	0.62
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1794275; hg19: chr6-32671248;