6-31240833-G-T

Variant names:

• chr6-31240833-G-T
• rs3132496

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 0.544 in 152,050 control chromosomes in the GnomAD database, including 22,575 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 0.54 (22575 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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: 0.544 AC: 82678 AN: 151932 Hom.: 22563 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.544 AC: 82726 AN: 152050 Hom.: 22575 Cov.: 32 AF XY: 0.539 AC XY: 40049 AN XY: 74294

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.517

Alfa AF: 0.546 Hom.: 18211

Bravo AF: 0.548

Asia WGS AF: 0.476 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.8
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132496; hg19: chr6-31208610;