chr2-55746597-C-T

Variant names:

• chr2-55746597-C-T
• rs2163237

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 0.297 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.297 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

African (AFR) AF: 0.169 AC: 6844 AN: 40610

American (AMR) AF: 0.327 AC: 4916 AN: 15046

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1420 AN: 3464

East Asian (EAS) AF: 0.716 AC: 3673 AN: 5130

South Asian (SAS) AF: 0.329 AC: 1549 AN: 4708

European-Finnish (FIN) AF: 0.320 AC: 3199 AN: 9994

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.322 AC: 21787 AN: 67592

Other (OTH) AF: 0.316 AC: 656 AN: 2078

Alfa AF: 0.314 Hom.: 20427

Bravo AF: 0.295

Asia WGS AF: 0.466 AC: 1618 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	2.3
DANN	Benign	0.90
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2163237; hg19: chr2-55973732;