rs4954391

Variant names:

• chr2-136126253-C-T
• rs4954391

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 0.712 in 152,178 control chromosomes in the GnomAD database, including 39,879 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 0.71 (39879 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.939 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: 0.712 AC: 108298 AN: 152060 Hom.: 39872 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.712 AC: 108347 AN: 152178 Hom.: 39879 Cov.: 33 AF XY: 0.719 AC XY: 53477 AN XY: 74418

African (AFR) AF: 0.527 AC: 21875 AN: 41474

American (AMR) AF: 0.720 AC: 11010 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2950 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4989 AN: 5188

South Asian (SAS) AF: 0.720 AC: 3475 AN: 4824

European-Finnish (FIN) AF: 0.873 AC: 9254 AN: 10604

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52309 AN: 68008

Other (OTH) AF: 0.744 AC: 1571 AN: 2112

Alfa AF: 0.760 Hom.: 68292

Bravo AF: 0.694

Asia WGS AF: 0.826 AC: 2875 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	2.7
DANN	Benign	0.71
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs4954391; hg19: chr2-136883823; COSMIC: COSV53891189;