6-31240833-G-T

Variant names:

• chr6-31240833-G-T
• rs3132496

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 0.544 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.529 AC: 21938 AN: 41470

American (AMR) AF: 0.536 AC: 8185 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3472

East Asian (EAS) AF: 0.588 AC: 3040 AN: 5174

South Asian (SAS) AF: 0.445 AC: 2144 AN: 4822

European-Finnish (FIN) AF: 0.465 AC: 4911 AN: 10560

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38454 AN: 67968

Other (OTH) AF: 0.517 AC: 1092 AN: 2114

Alfa AF: 0.562 Hom.: 66308

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3132496; hg19: chr6-31208610;