NM_130783.5:c.-152-26282A>G

Variant names:

• chr11-44834046-A-G
• rs11038172
• NM_130783.5:c.-152-26282A>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.-152-26282A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0593 in 151,684 control chromosomes in the GnomAD database, including 1,514 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 0.059 (1514 hom., cov: 30)
• Consequence: TSPAN18 NM_130783.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSPAN18	NM_130783.5	c.-152-26282A>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.-152-26282A>G		intron_variant	Intron 2 of 9	5	NM_130783.5	ENSP00000429993.2

Frequencies

GnomAD3 genomes AF: 0.0592 AC: 8979 AN: 151564 Hom.: 1504 Cov.: 30

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.00722

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00838

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0593 AC: 9001 AN: 151684 Hom.: 1514 Cov.: 30 AF XY: 0.0667 AC XY: 4940 AN XY: 74080

African (AFR) AF: 0.0255 AC: 1055 AN: 41326

American (AMR) AF: 0.242 AC: 3660 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.00722 AC: 25 AN: 3464

East Asian (EAS) AF: 0.593 AC: 3060 AN: 5158

South Asian (SAS) AF: 0.0576 AC: 276 AN: 4788

European-Finnish (FIN) AF: 0.0195 AC: 205 AN: 10516

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00838 AC: 570 AN: 67986

Other (OTH) AF: 0.0673 AC: 142 AN: 2110

Alfa AF: 0.0387 Hom.: 772

Bravo AF: 0.0787

Asia WGS AF: 0.289 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.39
DANN	Benign	0.35
PhyloP100		-1.4
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: rs11038172; hg19: chr11-44855597;