rs1346652

Positions:

• chr2-184963225-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;