rs11873284

Variant names:

• chr18-21135030-A-G
• rs11873284

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 0.172 in 152,140 control chromosomes in the GnomAD database, including 5,044 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 0.17 (5044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 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: 0.171 AC: 26049 AN: 152022 Hom.: 5019 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.172 AC: 26143 AN: 152140 Hom.: 5044 Cov.: 32 AF XY: 0.168 AC XY: 12532 AN XY: 74376

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.0887

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0550 Hom.: 794

Bravo AF: 0.199

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11873284; hg19: chr18-18714991;