chr18-73802432-C-T

Variant names:

• chr18-73802432-C-T
• rs1430540

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.51 in 151,924 control chromosomes in the GnomAD database, including 20,791 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 0.51 (20791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.603 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: 0.510 AC: 77382 AN: 151806 Hom.: 20786 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.510 AC: 77417 AN: 151924 Hom.: 20791 Cov.: 32 AF XY: 0.509 AC XY: 37783 AN XY: 74254

African (AFR) AF: 0.333 AC: 13786 AN: 41418

American (AMR) AF: 0.535 AC: 8174 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2099 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2911 AN: 5164

South Asian (SAS) AF: 0.622 AC: 2991 AN: 4810

European-Finnish (FIN) AF: 0.521 AC: 5486 AN: 10528

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40140 AN: 67948

Other (OTH) AF: 0.520 AC: 1098 AN: 2110

Alfa AF: 0.551 Hom.: 32145

Bravo AF: 0.500

Asia WGS AF: 0.590 AC: 2028 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.44
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1430540; hg19: chr18-71469667; COSMIC: COSV55923348;