rs2119154

Variant names:

• chr2-193490855-A-T
• rs2119154

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 0.152 in 152,114 control chromosomes in the GnomAD database, including 2,411 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 0.15 (2411 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 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: 0.152 AC: 23149 AN: 151996 Hom.: 2399 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0894

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.0972

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.152 AC: 23196 AN: 152114 Hom.: 2411 Cov.: 32 AF XY: 0.154 AC XY: 11448 AN XY: 74382

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.0830

Gnomad4 ASJ AF: 0.0649

Gnomad4 EAS AF: 0.0971

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0916

Gnomad4 OTH AF: 0.137

Alfa AF: 0.126 Hom.: 214

Bravo AF: 0.154

Asia WGS AF: 0.117 AC: 403 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2119154; hg19: chr2-194355580;