2-225373194-C-T

Variant names:

• chr2-225373194-C-T
• rs1517484

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 0.443 in 150,716 control chromosomes in the GnomAD database, including 15,026 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 0.44 (15026 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 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: 0.443 AC: 66745 AN: 150600 Hom.: 15009 Cov.: 29

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.443 AC: 66807 AN: 150716 Hom.: 15026 Cov.: 29 AF XY: 0.437 AC XY: 32171 AN XY: 73544

African (AFR) AF: 0.502 AC: 20627 AN: 41108

American (AMR) AF: 0.364 AC: 5492 AN: 15082

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1593 AN: 3456

East Asian (EAS) AF: 0.204 AC: 1043 AN: 5112

South Asian (SAS) AF: 0.320 AC: 1530 AN: 4782

European-Finnish (FIN) AF: 0.459 AC: 4678 AN: 10182

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30393 AN: 67690

Other (OTH) AF: 0.441 AC: 926 AN: 2098

Alfa AF: 0.442 Hom.: 49741

Bravo AF: 0.433

Asia WGS AF: 0.288 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.70
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs1517484; hg19: chr2-226237910;