rs1789110

Positions:

• chr18-77147088-C-A
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;