18-74533065-C-T

Variant names:

• chr18-74533065-C-T
• rs890332

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 0.797 in 152,148 control chromosomes in the GnomAD database, including 49,945 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 (49945 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

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 = 0.901 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: 0.797 AC: 121232 AN: 152030 Hom.: 49936 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.797 AC: 121285 AN: 152148 Hom.: 49945 Cov.: 31 AF XY: 0.800 AC XY: 59506 AN XY: 74408

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.802

Alfa AF: 0.805 Hom.: 4856

Bravo AF: 0.784

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	-0.96
CADD	Benign	0.76
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs890332; hg19: chr18-72200300;