6-31251058-A-G

Variant names:

• chr6-31251058-A-G
• rs4084090

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 0.0867 in 152,190 control chromosomes in the GnomAD database, including 656 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 0.087 (656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13175 AN: 152072 Hom.: 650 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0910

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0867 AC: 13199 AN: 152190 Hom.: 656 Cov.: 32 AF XY: 0.0876 AC XY: 6516 AN XY: 74420

African (AFR) AF: 0.124 AC: 5165 AN: 41500

American (AMR) AF: 0.0908 AC: 1388 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.0746 AC: 387 AN: 5190

South Asian (SAS) AF: 0.141 AC: 679 AN: 4832

European-Finnish (FIN) AF: 0.0421 AC: 446 AN: 10592

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4623 AN: 68004

Other (OTH) AF: 0.107 AC: 226 AN: 2116

Alfa AF: 0.0724 Hom.: 860

Bravo AF: 0.0939

Asia WGS AF: 0.119 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.80
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4084090; hg19: chr6-31218835;