rs12954572

Variant names:

• chr18-76111598-C-T
• rs12954572

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 0.185 in 152,144 control chromosomes in the GnomAD database, including 2,644 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 0.19 (2644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 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: 0.185 AC: 28179 AN: 152024 Hom.: 2649 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.185 AC: 28171 AN: 152144 Hom.: 2644 Cov.: 32 AF XY: 0.189 AC XY: 14059 AN XY: 74370

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.185

Alfa AF: 0.192 Hom.: 2208

Bravo AF: 0.181

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12954572; hg19: chr18-73823553; COSMIC: COSV61585548;