rs1789094

Variant names:

• chr18-77134229-C-T
• rs1789094

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 0.236 in 152,058 control chromosomes in the GnomAD database, including 4,385 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 0.24 (4385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 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: 0.236 AC: 35838 AN: 151938 Hom.: 4381 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.236 AC: 35864 AN: 152058 Hom.: 4385 Cov.: 32 AF XY: 0.236 AC XY: 17557 AN XY: 74306

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.256

Alfa AF: 0.210 Hom.: 4304

Bravo AF: 0.241

Asia WGS AF: 0.304 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789094; hg19: chr18-74846185;