rs11082098

Positions:

• chr18-38618768-C-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 0.0805 in 152,012 control chromosomes in the GnomAD database, including 655 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 0.080 (655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 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: 0.0803 AC: 12204 AN: 151892 Hom.: 647 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0286

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0929

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0805 AC: 12231 AN: 152012 Hom.: 655 Cov.: 32 AF XY: 0.0846 AC XY: 6284 AN XY: 74288

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0286

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0929

Gnomad4 NFE AF: 0.0647

Gnomad4 OTH AF: 0.0754

Alfa AF: 0.0701 Hom.: 206

Bravo AF: 0.0859

Asia WGS AF: 0.172 AC: 595 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11082098; hg19: chr18-36198732; COSMIC: COSV57483257;