chr2-139942390-T-A

Variant names:

• chr2-139942390-T-A
• rs4954808

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 0.672 in 151,924 control chromosomes in the GnomAD database, including 34,449 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 0.67 (34449 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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: 0.671 AC: 101920 AN: 151804 Hom.: 34404 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.672 AC: 102020 AN: 151924 Hom.: 34449 Cov.: 31 AF XY: 0.679 AC XY: 50435 AN XY: 74262

African (AFR) AF: 0.645 AC: 26702 AN: 41422

American (AMR) AF: 0.744 AC: 11337 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2075 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4111 AN: 5166

South Asian (SAS) AF: 0.742 AC: 3580 AN: 4828

European-Finnish (FIN) AF: 0.750 AC: 7893 AN: 10524

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44039 AN: 67968

Other (OTH) AF: 0.680 AC: 1434 AN: 2110

Alfa AF: 0.661 Hom.: 4155

Bravo AF: 0.672

Asia WGS AF: 0.750 AC: 2594 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.27
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs4954808; hg19: chr2-140699959;