rs1789139

Variant names:

• chr18-77168012-G-A
• rs1789139

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 0.118 in 152,188 control chromosomes in the GnomAD database, including 1,101 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 0.12 (1101 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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: 0.117 AC: 17865 AN: 152070 Hom.: 1087 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.118 AC: 17928 AN: 152188 Hom.: 1101 Cov.: 33 AF XY: 0.118 AC XY: 8761 AN XY: 74402

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.0873

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.126

Alfa AF: 0.105 Hom.: 397

Bravo AF: 0.117

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789139; hg19: chr18-74879968;