6-131802584-G-T

Variant names:

• chr6-131802584-G-T
• rs13211931

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 0.0471 in 152,142 control chromosomes in the GnomAD database, including 193 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 0.047 (193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0724 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: 0.0470 AC: 7145 AN: 152024 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0743

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0378

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0471 AC: 7164 AN: 152142 Hom.: 193 Cov.: 32 AF XY: 0.0465 AC XY: 3461 AN XY: 74380

African (AFR) AF: 0.0746 AC: 3098 AN: 41514

American (AMR) AF: 0.0487 AC: 744 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3470

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5172

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4814

European-Finnish (FIN) AF: 0.0159 AC: 168 AN: 10596

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0378 AC: 2571 AN: 67986

Other (OTH) AF: 0.0610 AC: 129 AN: 2114

Alfa AF: 0.0365 Hom.: 108

Bravo AF: 0.0522

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.45
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs13211931; hg19: chr6-132123724;