2-181454574-C-T

Variant names:

• chr2-181454574-C-T
• rs1449263

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 0.555 in 151,978 control chromosomes in the GnomAD database, including 23,741 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 0.55 (23741 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 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: 0.555 AC: 84280 AN: 151860 Hom.: 23722 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.555 AC: 84343 AN: 151978 Hom.: 23741 Cov.: 31 AF XY: 0.558 AC XY: 41458 AN XY: 74294

African (AFR) AF: 0.583 AC: 24173 AN: 41438

American (AMR) AF: 0.543 AC: 8302 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1698 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1863 AN: 5152

South Asian (SAS) AF: 0.600 AC: 2888 AN: 4810

European-Finnish (FIN) AF: 0.610 AC: 6454 AN: 10572

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37144 AN: 67952

Other (OTH) AF: 0.546 AC: 1148 AN: 2104

Alfa AF: 0.543 Hom.: 89736

Bravo AF: 0.550

Asia WGS AF: 0.481 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1449263; hg19: chr2-182319301;