2-182800434-T-C

Variant names:

• chr2-182800434-T-C
• rs1452312

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 0.627 in 152,014 control chromosomes in the GnomAD database, including 30,421 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 0.63 (30421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.706 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: 0.627 AC: 95239 AN: 151896 Hom.: 30406 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.627 AC: 95300 AN: 152014 Hom.: 30421 Cov.: 32 AF XY: 0.620 AC XY: 46087 AN XY: 74286

African (AFR) AF: 0.712 AC: 29542 AN: 41468

American (AMR) AF: 0.579 AC: 8837 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1950 AN: 5174

South Asian (SAS) AF: 0.618 AC: 2979 AN: 4820

European-Finnish (FIN) AF: 0.544 AC: 5745 AN: 10558

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41614 AN: 67958

Other (OTH) AF: 0.645 AC: 1358 AN: 2106

Alfa AF: 0.498 Hom.: 1400

Bravo AF: 0.628

Asia WGS AF: 0.534 AC: 1864 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.59
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1452312; hg19: chr2-183665161;