rs10947332

Variant names:

• chr6-32709663-G-A
• rs10947332

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.141

Alfa AF: 0.116 Hom.: 937

Bravo AF: 0.128

Asia WGS AF: 0.117 AC: 412 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10947332; hg19: chr6-32677440;