rs11873891

Variant names:

• chr18-6505598-G-A
• rs11873891

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;