2-82596701-C-T

Variant names:

• chr2-82596701-C-T
• rs2862972

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 0.25 in 114,196 control chromosomes in the GnomAD database, including 3,054 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 0.25 (3054 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.250 AC: 28595 AN: 114166 Hom.: 3056 Cov.: 25

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.250 AC: 28589 AN: 114196 Hom.: 3054 Cov.: 25 AF XY: 0.250 AC XY: 13615 AN XY: 54404

African (AFR) AF: 0.304 AC: 9757 AN: 32106

American (AMR) AF: 0.229 AC: 2458 AN: 10726

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 551 AN: 2836

East Asian (EAS) AF: 0.0688 AC: 208 AN: 3022

South Asian (SAS) AF: 0.160 AC: 518 AN: 3230

European-Finnish (FIN) AF: 0.225 AC: 1295 AN: 5758

Middle Eastern (MID) AF: 0.278 AC: 55 AN: 198

European-Non Finnish (NFE) AF: 0.246 AC: 13287 AN: 54116

Other (OTH) AF: 0.233 AC: 357 AN: 1534

Alfa AF: 0.200 Hom.: 4828

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.056
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs2862972; hg19: chr2-82823825;