chr6-32447303-G-A

Variant names:

• chr6-32447303-G-A
• rs3129891

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 0.204 in 152,040 control chromosomes in the GnomAD database, including 3,226 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 0.20 (3226 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 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: 0.204 AC: 31030 AN: 151922 Hom.: 3228 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.204 AC: 31042 AN: 152040 Hom.: 3226 Cov.: 31 AF XY: 0.202 AC XY: 15046 AN XY: 74310

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.207

Alfa AF: 0.210 Hom.: 3108

Bravo AF: 0.197

Asia WGS AF: 0.272 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129891; hg19: chr6-32415080;