rs3094564

Variant names:

• chr6-29518568-C-T
• rs3094564

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 0.634 in 151,956 control chromosomes in the GnomAD database, including 30,827 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 0.63 (30827 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96270 AN: 151838 Hom.: 30780 Cov.: 31

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.634 AC: 96374 AN: 151956 Hom.: 30827 Cov.: 31 AF XY: 0.637 AC XY: 47348 AN XY: 74294

African (AFR) AF: 0.686 AC: 28422 AN: 41434

American (AMR) AF: 0.568 AC: 8672 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3480 AN: 5156

South Asian (SAS) AF: 0.783 AC: 3774 AN: 4820

European-Finnish (FIN) AF: 0.673 AC: 7099 AN: 10556

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41258 AN: 67942

Other (OTH) AF: 0.610 AC: 1285 AN: 2108

Alfa AF: 0.618 Hom.: 68598

Bravo AF: 0.629

Asia WGS AF: 0.771 AC: 2682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.22
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3094564; hg19: chr6-29486345;