rs3131622

Positions:

• chr6-31452723-T-G

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 0.404 in 151,654 control chromosomes in the GnomAD database, including 13,056 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 0.40 (13056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61167 AN: 151534 Hom.: 13042 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.404 AC: 61223 AN: 151654 Hom.: 13056 Cov.: 32 AF XY: 0.401 AC XY: 29756 AN XY: 74114

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.381

Alfa AF: 0.416 Hom.: 12156

Bravo AF: 0.397

Asia WGS AF: 0.279 AC: 972 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131622; hg19: chr6-31420500;