2-189514024-C-T

Variant names:

• chr2-189514024-C-T
• rs744653

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 0.843 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.843 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

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.849

Alfa AF: 0.849 Hom.: 29464

Bravo AF: 0.847

Asia WGS AF: 0.854 AC: 2971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs744653; hg19: chr2-190378750;