rs3132531

Variant names:

• chr6-31233695-C-T
• rs3132531

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 0.225 in 152,118 control chromosomes in the GnomAD database, including 4,001 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 0.23 (4001 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 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: 0.225 AC: 34241 AN: 152000 Hom.: 4000 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.225 AC: 34248 AN: 152118 Hom.: 4001 Cov.: 32 AF XY: 0.221 AC XY: 16437 AN XY: 74348

African (AFR) AF: 0.167 AC: 6926 AN: 41510

American (AMR) AF: 0.196 AC: 2997 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 997 AN: 3462

East Asian (EAS) AF: 0.282 AC: 1461 AN: 5174

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4824

European-Finnish (FIN) AF: 0.180 AC: 1908 AN: 10572

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18018 AN: 67990

Other (OTH) AF: 0.237 AC: 500 AN: 2108

Alfa AF: 0.236 Hom.: 571

Bravo AF: 0.223

Asia WGS AF: 0.220 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.96
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs3132531; hg19: chr6-31201472;