rs1789110

Variant names:

• chr18-77147088-C-A
• rs1789110
• ENST00000839177.1:n.*131G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-77147088-C-A
• chr18-77147088-C-G
• chr18-77147088-C-T

Variant summary

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

The ENST00000839177.1(ENSG00000309160):​n.*131G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,112 control chromosomes in the GnomAD database, including 29,910 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 0.62 (29910 hom., cov: 32)
• Consequence: ENSG00000309160 ENST00000839177.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.35
• Publications: 13 publications found

Genes affected

ENSG00000309160 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839177.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309160	ENST00000839177.1		n.*131G>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94870 AN: 151994 Hom.: 29891 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.624 AC: 94939 AN: 152112 Hom.: 29910 Cov.: 32 AF XY: 0.621 AC XY: 46149 AN XY: 74346

African (AFR) AF: 0.708 AC: 29372 AN: 41492

American (AMR) AF: 0.563 AC: 8605 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2848 AN: 5168

South Asian (SAS) AF: 0.654 AC: 3155 AN: 4822

European-Finnish (FIN) AF: 0.554 AC: 5859 AN: 10576

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40942 AN: 67982

Other (OTH) AF: 0.623 AC: 1316 AN: 2114

Alfa AF: 0.608 Hom.: 97249

Bravo AF: 0.629

Asia WGS AF: 0.630 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.36
PhyloP100		-5.3

Splicing

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

Other links and lift over

dbSNP: rs1789110; hg19: chr18-74859044;