2-53275637-A-G

Variant names:

• chr2-53275637-A-G
• rs996712

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 0.302 in 151,778 control chromosomes in the GnomAD database, including 8,714 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 0.30 (8714 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 8 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 = 0.527 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: 0.302 AC: 45793 AN: 151656 Hom.: 8674 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.302 AC: 45895 AN: 151778 Hom.: 8714 Cov.: 31 AF XY: 0.301 AC XY: 22290 AN XY: 74130

African (AFR) AF: 0.533 AC: 22010 AN: 41330

American (AMR) AF: 0.326 AC: 4964 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 851 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1424 AN: 5138

South Asian (SAS) AF: 0.283 AC: 1356 AN: 4794

European-Finnish (FIN) AF: 0.142 AC: 1499 AN: 10546

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13005 AN: 67964

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.236 Hom.: 15023

Bravo AF: 0.324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.65
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs996712; hg19: chr2-53502775;