chr3-94524869-G-A

Variant names:

• chr3-94524869-G-A
• rs13067306

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 0.165 in 151,814 control chromosomes in the GnomAD database, including 2,402 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 0.17 (2402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 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: 0.165 AC: 25074 AN: 151720 Hom.: 2405 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.0584

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.165 AC: 25072 AN: 151814 Hom.: 2402 Cov.: 32 AF XY: 0.165 AC XY: 12223 AN XY: 74144

African (AFR) AF: 0.0850 AC: 3522 AN: 41452

American (AMR) AF: 0.193 AC: 2946 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3472

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5172

South Asian (SAS) AF: 0.190 AC: 910 AN: 4802

European-Finnish (FIN) AF: 0.242 AC: 2525 AN: 10454

Middle Eastern (MID) AF: 0.0594 AC: 17 AN: 286

European-Non Finnish (NFE) AF: 0.210 AC: 14242 AN: 67930

Other (OTH) AF: 0.149 AC: 314 AN: 2104

Alfa AF: 0.191 Hom.: 5194

Bravo AF: 0.158

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs13067306; hg19: chr3-94243713;