18-74532924-A-G

Variant names:

• chr18-74532924-A-G
• rs12954438

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;