rs12652255

Variant names:

• chr5-175334092-C-A
• rs12652255

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 0.149 in 152,070 control chromosomes in the GnomAD database, including 2,062 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 0.15 (2062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 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: 0.149 AC: 22678 AN: 151952 Hom.: 2058 Cov.: 32

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.149 AC: 22690 AN: 152070 Hom.: 2062 Cov.: 32 AF XY: 0.152 AC XY: 11334 AN XY: 74336

African (AFR) AF: 0.0606 AC: 2515 AN: 41516

American (AMR) AF: 0.186 AC: 2842 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1464 AN: 5102

South Asian (SAS) AF: 0.274 AC: 1321 AN: 4824

European-Finnish (FIN) AF: 0.162 AC: 1710 AN: 10584

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11182 AN: 67980

Other (OTH) AF: 0.169 AC: 355 AN: 2106

Alfa AF: 0.159 Hom.: 4742

Bravo AF: 0.147

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs12652255; hg19: chr5-174761095;