rs835784

Variant names:

• chr11-44842267-A-G
• rs835784
• NM_130783.5:c.-152-18061A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130783.5(TSPAN18):​c.-152-18061A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,086 control chromosomes in the GnomAD database, including 20,984 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 0.52 (20984 hom., cov: 32)
• Consequence: TSPAN18 NM_130783.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 15 publications found

Genes affected

TSPAN18 (HGNC:20660): (tetraspanin 18) Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TSPAN18 Gene-Disease associations (from GenCC):

• intellectual disability

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000296707 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSPAN18	NM_130783.5	c.-152-18061A>G		intron_variant	Intron 2 of 9	ENST00000520358.7	NP_570139.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPAN18	ENST00000520358.7	c.-152-18061A>G		intron_variant	Intron 2 of 9	5	NM_130783.5	ENSP00000429993.2

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79206 AN: 151968 Hom.: 20937 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.521 AC: 79305 AN: 152086 Hom.: 20984 Cov.: 32 AF XY: 0.526 AC XY: 39135 AN XY: 74346

African (AFR) AF: 0.482 AC: 20013 AN: 41482

American (AMR) AF: 0.644 AC: 9849 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1772 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3872 AN: 5172

South Asian (SAS) AF: 0.564 AC: 2716 AN: 4816

European-Finnish (FIN) AF: 0.556 AC: 5887 AN: 10584

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33482 AN: 67956

Other (OTH) AF: 0.524 AC: 1107 AN: 2114

Alfa AF: 0.507 Hom.: 89455

Bravo AF: 0.528

Asia WGS AF: 0.653 AC: 2270 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	1.4
DANN	Benign	0.58
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs835784; hg19: chr11-44863818;