chr2-82625500-A-G

Variant names:

• chr2-82625500-A-G
• rs7608203

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 0.333 in 152,044 control chromosomes in the GnomAD database, including 9,855 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 0.33 (9855 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50640 AN: 151924 Hom.: 9839 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.333 AC: 50692 AN: 152044 Hom.: 9855 Cov.: 33 AF XY: 0.327 AC XY: 24330 AN XY: 74338

African (AFR) AF: 0.529 AC: 21898 AN: 41434

American (AMR) AF: 0.253 AC: 3862 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3472

East Asian (EAS) AF: 0.0431 AC: 223 AN: 5170

South Asian (SAS) AF: 0.186 AC: 899 AN: 4824

European-Finnish (FIN) AF: 0.231 AC: 2444 AN: 10588

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19376 AN: 67964

Other (OTH) AF: 0.302 AC: 638 AN: 2114

Alfa AF: 0.271 Hom.: 2981

Bravo AF: 0.342

Asia WGS AF: 0.133 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7608203; hg19: chr2-82852624;