2-136240824-C-T

Variant names:

• chr2-136240824-C-T
• rs4954585

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 0.548 in 151,944 control chromosomes in the GnomAD database, including 24,598 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 0.55 (24598 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.669 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: 0.548 AC: 83216 AN: 151826 Hom.: 24608 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.548 AC: 83233 AN: 151944 Hom.: 24598 Cov.: 31 AF XY: 0.540 AC XY: 40071 AN XY: 74258

African (AFR) AF: 0.422 AC: 17479 AN: 41412

American (AMR) AF: 0.448 AC: 6840 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3470

East Asian (EAS) AF: 0.167 AC: 860 AN: 5162

South Asian (SAS) AF: 0.410 AC: 1974 AN: 4814

European-Finnish (FIN) AF: 0.676 AC: 7128 AN: 10546

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.674 AC: 45841 AN: 67966

Other (OTH) AF: 0.479 AC: 1006 AN: 2102

Alfa AF: 0.611 Hom.: 97130

Bravo AF: 0.527

Asia WGS AF: 0.302 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.60
DANN	Benign	0.61
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs4954585; hg19: chr2-136998394;