2-53275637-A-G

Position:

• chr2-53275637-A-G

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 0.302 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53275637A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.286

Alfa AF: 0.215 Hom.: 7795

Bravo AF: 0.324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996712; hg19: chr2-53502775;