2-136240824-C-T

Variant names:

• chr2-136240824-C-T
• rs4954585

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.479

Alfa AF: 0.604 Hom.: 38977

Bravo AF: 0.527

Asia WGS AF: 0.302 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4954585; hg19: chr2-136998394;