6-31353346-G-T

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 0.886 in 151,658 control chromosomes in the GnomAD database, including 59,585 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 0.89 (59585 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.886 AC: 134216 AN: 151540 Hom.: 59525 Cov.: 28

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.886 AC: 134333 AN: 151658 Hom.: 59585 Cov.: 28 AF XY: 0.889 AC XY: 65898 AN XY: 74098

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.963

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.917

Alfa AF: 0.868 Hom.: 16118

Bravo AF: 0.891

Asia WGS AF: 0.961 AC: 3343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.18
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523612; hg19: chr6-31321123;