rs1346652

Variant names:

• chr2-184963225-T-C
• rs1346652

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 0.157 in 151,948 control chromosomes in the GnomAD database, including 2,887 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 0.16 (2887 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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: 0.157 AC: 23782 AN: 151830 Hom.: 2871 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.157 AC: 23827 AN: 151948 Hom.: 2887 Cov.: 32 AF XY: 0.153 AC XY: 11329 AN XY: 74270

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0340

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0443

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.155

Alfa AF: 0.127 Hom.: 240

Bravo AF: 0.167

Asia WGS AF: 0.0850 AC: 294 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1346652; hg19: chr2-185827952;