rs12954438

Positions:

• chr18-74532924-A-G
• chr18-74532924-A-T

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 0.798 in 152,148 control chromosomes in the GnomAD database, including 50,054 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 0.80 (50054 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.74532924A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121431 AN: 152030 Hom.: 50044 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.798 AC: 121486 AN: 152148 Hom.: 50054 Cov.: 32 AF XY: 0.801 AC XY: 59586 AN XY: 74388

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.804

Alfa AF: 0.814 Hom.: 4455

Bravo AF: 0.785

Asia WGS AF: 0.900 AC: 3129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12954438; hg19: chr18-72200159;