rs11873891

chr18-6505598-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 0.577 in 152,034 control chromosomes in the GnomAD database, including 25,834 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 0.58 (25834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 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: 0.577 AC: 87580 AN: 151916 Hom.: 25801 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.577 AC: 87657 AN: 152034 Hom.: 25834 Cov.: 32 AF XY: 0.569 AC XY: 42289 AN XY: 74310

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.597

Alfa AF: 0.605 Hom.: 17085

Bravo AF: 0.582

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.4
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11873891; hg19: chr18-6505597;