rs2602044

Variant names:

• chr3-108226346-A-T
• rs2602044

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 0.861 in 152,166 control chromosomes in the GnomAD database, including 57,349 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 (57349 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.94 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: 0.861 AC: 130961 AN: 152048 Hom.: 57329 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.861 AC: 131028 AN: 152166 Hom.: 57349 Cov.: 32 AF XY: 0.854 AC XY: 63493 AN XY: 74380

African (AFR) AF: 0.780 AC: 32344 AN: 41484

American (AMR) AF: 0.801 AC: 12244 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3341 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2449 AN: 5170

South Asian (SAS) AF: 0.807 AC: 3891 AN: 4822

European-Finnish (FIN) AF: 0.887 AC: 9391 AN: 10586

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.946 AC: 64346 AN: 68026

Other (OTH) AF: 0.874 AC: 1848 AN: 2114

Alfa AF: 0.904 Hom.: 7792

Bravo AF: 0.851

Asia WGS AF: 0.633 AC: 2205 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.74
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs2602044; hg19: chr3-107945193;