2-82438552-C-T

Variant names:

• chr2-82438552-C-T
• rs1365951

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 0.498 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.467

Alfa AF: 0.385 Hom.: 15960

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365951; hg19: chr2-82665676;