2-55746597-C-T

Variant names:

• chr2-55746597-C-T
• rs2163237

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 0.297 in 149,826 control chromosomes in the GnomAD database, including 7,514 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 0.30 (7514 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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: 0.297 AC: 44505 AN: 149716 Hom.: 7498 Cov.: 28

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.297 AC: 44547 AN: 149826 Hom.: 7514 Cov.: 28 AF XY: 0.303 AC XY: 22147 AN XY: 72998

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.316

Alfa AF: 0.310 Hom.: 7723

Bravo AF: 0.295

Asia WGS AF: 0.466 AC: 1618 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	2.3
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2163237; hg19: chr2-55973732;