rs3135005

Variant names:

• chr6-32618242-A-G
• rs3135005

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 0.862 in 152,056 control chromosomes in the GnomAD database, including 56,645 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 0.86 (56645 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.899 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: 0.862 AC: 131041 AN: 151938 Hom.: 56600 Cov.: 30

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.862 AC: 131143 AN: 152056 Hom.: 56645 Cov.: 30 AF XY: 0.861 AC XY: 64027 AN XY: 74330

African (AFR) AF: 0.853 AC: 35324 AN: 41412

American (AMR) AF: 0.912 AC: 13946 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3239 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4438 AN: 5172

South Asian (SAS) AF: 0.780 AC: 3750 AN: 4808

European-Finnish (FIN) AF: 0.871 AC: 9225 AN: 10590

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58230 AN: 67986

Other (OTH) AF: 0.891 AC: 1884 AN: 2114

Alfa AF: 0.866 Hom.: 60238

Bravo AF: 0.869

Asia WGS AF: 0.790 AC: 2751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.9
DANN	Benign	0.62
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs3135005; hg19: chr6-32586019;