18-9091546-C-T

Variant names:

• chr18-9091546-C-T
• rs12964485

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 0.297 in 151,376 control chromosomes in the GnomAD database, including 7,674 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 0.30 (7674 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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: 0.297 AC: 44902 AN: 151266 Hom.: 7674 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.297 AC: 44910 AN: 151376 Hom.: 7674 Cov.: 31 AF XY: 0.303 AC XY: 22387 AN XY: 73908

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.293

Alfa AF: 0.327 Hom.: 4752

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.85
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12964485; hg19: chr18-9091544;