chr2-52486669-T-G

Position:

• chr2-52486669-T-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 0.203 in 152,016 control chromosomes in the GnomAD database, including 3,555 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 0.20 (3555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30904 AN: 151898 Hom.: 3552 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.203 AC: 30904 AN: 152016 Hom.: 3555 Cov.: 32 AF XY: 0.199 AC XY: 14749 AN XY: 74296

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0122

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.195

Alfa AF: 0.223 Hom.: 509

Bravo AF: 0.195

Asia WGS AF: 0.0960 AC: 334 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1526687; hg19: chr2-52713807;