rs1349882

Positions:

• chr2-52722180-G-T

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 0.407 in 151,988 control chromosomes in the GnomAD database, including 12,831 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 0.41 (12831 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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: 0.407 AC: 61784 AN: 151870 Hom.: 12818 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.407 AC: 61823 AN: 151988 Hom.: 12831 Cov.: 33 AF XY: 0.409 AC XY: 30393 AN XY: 74276

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.416

Alfa AF: 0.393 Hom.: 14466

Bravo AF: 0.405

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1349882; hg19: chr2-52949318;