6-32709663-G-A

Variant names:

• chr6-32709663-G-A
• rs10947332

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 0.134 in 152,012 control chromosomes in the GnomAD database, including 1,455 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 0.13 (1455 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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: 0.134 AC: 20363 AN: 151894 Hom.: 1451 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0917

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.134 AC: 20390 AN: 152012 Hom.: 1455 Cov.: 31 AF XY: 0.137 AC XY: 10152 AN XY: 74308

African (AFR) AF: 0.154 AC: 6386 AN: 41458

American (AMR) AF: 0.116 AC: 1774 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3472

East Asian (EAS) AF: 0.145 AC: 746 AN: 5158

South Asian (SAS) AF: 0.0934 AC: 450 AN: 4818

European-Finnish (FIN) AF: 0.208 AC: 2190 AN: 10552

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7864 AN: 67974

Other (OTH) AF: 0.141 AC: 296 AN: 2104

Alfa AF: 0.121 Hom.: 2119

Bravo AF: 0.128

Asia WGS AF: 0.117 AC: 412 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.52
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10947332; hg19: chr6-32677440;