rs1346652

Variant names:

• chr2-184963225-T-C
• rs1346652

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.340 AC: 14087 AN: 41444

American (AMR) AF: 0.101 AC: 1545 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 401 AN: 3472

East Asian (EAS) AF: 0.0340 AC: 174 AN: 5120

South Asian (SAS) AF: 0.123 AC: 592 AN: 4820

European-Finnish (FIN) AF: 0.0443 AC: 470 AN: 10604

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.0904 AC: 6144 AN: 67942

Other (OTH) AF: 0.155 AC: 326 AN: 2110

Alfa AF: 0.135 Hom.: 285

Bravo AF: 0.167

Asia WGS AF: 0.0850 AC: 294 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1346652; hg19: chr2-185827952;