2-82438552-C-T

Variant names:

• chr2-82438552-C-T
• rs1365951

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 0.498 in 151,814 control chromosomes in the GnomAD database, including 22,862 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 0.50 (22862 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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: 0.498 AC: 75536 AN: 151698 Hom.: 22807 Cov.: 31

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.498 AC: 75654 AN: 151814 Hom.: 22862 Cov.: 31 AF XY: 0.490 AC XY: 36386 AN XY: 74182

African (AFR) AF: 0.862 AC: 35745 AN: 41446

American (AMR) AF: 0.402 AC: 6127 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1382 AN: 3466

East Asian (EAS) AF: 0.356 AC: 1832 AN: 5144

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4810

European-Finnish (FIN) AF: 0.314 AC: 3302 AN: 10516

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24456 AN: 67892

Other (OTH) AF: 0.467 AC: 979 AN: 2096

Alfa AF: 0.405 Hom.: 40515

Bravo AF: 0.524

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.24
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1365951; hg19: chr2-82665676;