rs1789103

Variant names:

• chr18-77153783-C-A
• rs1789103

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 0.275 in 152,076 control chromosomes in the GnomAD database, including 6,296 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 0.28 (6296 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.408 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: 0.276 AC: 41872 AN: 151958 Hom.: 6292 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.275 AC: 41892 AN: 152076 Hom.: 6296 Cov.: 33 AF XY: 0.282 AC XY: 20957 AN XY: 74322

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.281

Alfa AF: 0.221 Hom.: 2654

Bravo AF: 0.285

Asia WGS AF: 0.439 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789103; hg19: chr18-74865739;