2-136278108-G-A

Variant names:

• chr2-136278108-G-A
• rs4347891

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 0.835 in 152,166 control chromosomes in the GnomAD database, including 54,487 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 0.84 (54487 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.836 AC: 127072 AN: 152048 Hom.: 54476 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.835 AC: 127114 AN: 152166 Hom.: 54487 Cov.: 32 AF XY: 0.835 AC XY: 62081 AN XY: 74382

African (AFR) AF: 0.632 AC: 26205 AN: 41480

American (AMR) AF: 0.801 AC: 12240 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3082 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4260 AN: 5152

South Asian (SAS) AF: 0.887 AC: 4283 AN: 4830

European-Finnish (FIN) AF: 0.951 AC: 10083 AN: 10608

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 64048 AN: 68014

Other (OTH) AF: 0.838 AC: 1772 AN: 2114

Alfa AF: 0.819 Hom.: 24035

Bravo AF: 0.813

Asia WGS AF: 0.797 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs4347891; hg19: chr2-137035678;