rs12523475

Variant names:

• chr5-56360737-C-T
• rs12523475

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 0.119 in 152,202 control chromosomes in the GnomAD database, including 1,282 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 0.12 (1282 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 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: 0.119 AC: 18155 AN: 152084 Hom.: 1287 Cov.: 33

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.119 AC: 18133 AN: 152202 Hom.: 1282 Cov.: 33 AF XY: 0.119 AC XY: 8870 AN XY: 74414

African (AFR) AF: 0.0324 AC: 1347 AN: 41540

American (AMR) AF: 0.118 AC: 1802 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3470

East Asian (EAS) AF: 0.187 AC: 966 AN: 5178

South Asian (SAS) AF: 0.188 AC: 907 AN: 4818

European-Finnish (FIN) AF: 0.114 AC: 1206 AN: 10578

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10520 AN: 68000

Other (OTH) AF: 0.163 AC: 344 AN: 2114

Alfa AF: 0.152 Hom.: 1020

Bravo AF: 0.116

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.39
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12523475; hg19: chr5-55656564; COSMIC: COSV60134244;