rs1789094

Variant names:

• chr18-77134229-C-T
• rs1789094

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 0.236 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.301 AC: 12494 AN: 41470

American (AMR) AF: 0.226 AC: 3452 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5170

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4816

European-Finnish (FIN) AF: 0.217 AC: 2296 AN: 10562

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12922 AN: 67978

Other (OTH) AF: 0.256 AC: 539 AN: 2108

Alfa AF: 0.213 Hom.: 5508

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
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs1789094; hg19: chr18-74846185;