rs754789

Variant names:

• chr18-57534229-T-C
• rs754789

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 0.169 in 151,160 control chromosomes in the GnomAD database, including 2,266 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 0.17 (2266 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 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: 0.169 AC: 25547 AN: 151040 Hom.: 2270 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.169 AC: 25551 AN: 151160 Hom.: 2266 Cov.: 31 AF XY: 0.172 AC XY: 12694 AN XY: 73852

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0778

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.179

Alfa AF: 0.161 Hom.: 4239

Bravo AF: 0.157

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	0.69
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754789; hg19: chr18-55201461;