NM_130783.5:c.-152-14942T>C

Variant names:

• chr11-44845386-T-C
• rs835791
• NM_130783.5:c.-152-14942T>C

Variant summary

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

The NM_130783.5(TSPAN18):​c.-152-14942T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,274 control chromosomes in the GnomAD database, including 58,589 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 0.88 (58589 hom., cov: 34)
• Consequence: TSPAN18 NM_130783.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSPAN18	NM_130783.5	c.-152-14942T>C		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.-152-14942T>C		intron_variant	Intron 2 of 9	5	NM_130783.5	ENSP00000429993.2

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133383 AN: 152156 Hom.: 58526 Cov.: 34

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.877 AC: 133507 AN: 152274 Hom.: 58589 Cov.: 34 AF XY: 0.876 AC XY: 65193 AN XY: 74446

African (AFR) AF: 0.848 AC: 35212 AN: 41542

American (AMR) AF: 0.912 AC: 13961 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3134 AN: 3470

East Asian (EAS) AF: 0.929 AC: 4792 AN: 5156

South Asian (SAS) AF: 0.794 AC: 3837 AN: 4830

European-Finnish (FIN) AF: 0.887 AC: 9410 AN: 10612

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60234 AN: 68036

Other (OTH) AF: 0.895 AC: 1891 AN: 2114

Alfa AF: 0.880 Hom.: 29960

Bravo AF: 0.882

Asia WGS AF: 0.846 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.55
PhyloP100		-1.1
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: rs835791; hg19: chr11-44866937;