rs3132486

Positions:

• chr6-31275393-G-A

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 0.493 in 151,952 control chromosomes in the GnomAD database, including 18,637 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 0.49 (18637 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

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 (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74840 AN: 151834 Hom.: 18623 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.493 AC: 74891 AN: 151952 Hom.: 18637 Cov.: 31 AF XY: 0.491 AC XY: 36460 AN XY: 74264

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.470

Alfa AF: 0.503 Hom.: 1758

Bravo AF: 0.490

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132486; hg19: chr6-31243170;