rs1789103

Variant names:

• chr18-77153783-C-A
• rs1789103

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.362 AC: 14996 AN: 41468

American (AMR) AF: 0.345 AC: 5270 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3472

East Asian (EAS) AF: 0.395 AC: 2042 AN: 5170

South Asian (SAS) AF: 0.424 AC: 2038 AN: 4812

European-Finnish (FIN) AF: 0.275 AC: 2903 AN: 10560

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12641 AN: 67992

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.223 Hom.: 3306

Bravo AF: 0.285

Asia WGS AF: 0.439 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.61
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1789103; hg19: chr18-74865739;