rs1791303

chr18-59787994-G-A

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 0.364 in 151,934 control chromosomes in the GnomAD database, including 10,627 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 0.36 (10627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55286 AN: 151816 Hom.: 10609 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.364 AC: 55347 AN: 151934 Hom.: 10627 Cov.: 32 AF XY: 0.363 AC XY: 26963 AN XY: 74266

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.339

Alfa AF: 0.388 Hom.: 5702

Bravo AF: 0.367

Asia WGS AF: 0.322 AC: 1121 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.77
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1791303; hg19: chr18-57455226;