6-29137158-G-A

Variant names:

• chr6-29137158-G-A
• rs9295794

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 0.0808 in 151,920 control chromosomes in the GnomAD database, including 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 0.081 (575 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12276 AN: 151798 Hom.: 574 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0922

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0288

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0808 AC: 12280 AN: 151920 Hom.: 575 Cov.: 32 AF XY: 0.0815 AC XY: 6049 AN XY: 74246

African (AFR) AF: 0.0539 AC: 2234 AN: 41472

American (AMR) AF: 0.0970 AC: 1477 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3470

East Asian (EAS) AF: 0.0926 AC: 478 AN: 5162

South Asian (SAS) AF: 0.0746 AC: 359 AN: 4814

European-Finnish (FIN) AF: 0.107 AC: 1122 AN: 10532

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0885 AC: 6014 AN: 67934

Other (OTH) AF: 0.0860 AC: 181 AN: 2104

Alfa AF: 0.0806 Hom.: 644

Bravo AF: 0.0826

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.79
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs9295794; hg19: chr6-29104935;