rs1349882

Variant names:

• chr2-52722180-G-T
• rs1349882

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;