rs1789110

Variant names:

• chr18-77147088-C-A
• rs1789110

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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.35

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.624 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

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.623

Alfa AF: 0.608 Hom.: 37620

Bravo AF: 0.629

Asia WGS AF: 0.630 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789110; hg19: chr18-74859044;