chr2-189514024-C-T

Variant names:

• chr2-189514024-C-T
• rs744653

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 0.843 in 152,070 control chromosomes in the GnomAD database, including 54,264 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 0.84 (54264 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 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: 0.843 AC: 128126 AN: 151952 Hom.: 54225 Cov.: 30

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.843 AC: 128218 AN: 152070 Hom.: 54264 Cov.: 30 AF XY: 0.846 AC XY: 62861 AN XY: 74340

African (AFR) AF: 0.789 AC: 32717 AN: 41454

American (AMR) AF: 0.891 AC: 13612 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2938 AN: 3472

East Asian (EAS) AF: 0.977 AC: 5043 AN: 5160

South Asian (SAS) AF: 0.824 AC: 3970 AN: 4816

European-Finnish (FIN) AF: 0.856 AC: 9065 AN: 10590

Middle Eastern (MID) AF: 0.884 AC: 258 AN: 292

European-Non Finnish (NFE) AF: 0.854 AC: 58061 AN: 67994

Other (OTH) AF: 0.849 AC: 1790 AN: 2108

Alfa AF: 0.853 Hom.: 110178

Bravo AF: 0.847

Asia WGS AF: 0.854 AC: 2971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.85
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs744653; hg19: chr2-190378750;