Variant 11-44919322-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_130783.5(TSPAN18):c.432+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,607,982 control chromosomes in the GnomAD database, including 15,362 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.16 ( 2071 hom., cov: 33)

Exomes 𝑓: 0.13 ( 13291 hom. )

Consequence

TSPAN18
NM_130783.5 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.203

Variant links:

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 links:

TP53I11 (HGNC:16842): (tumor protein p53 inducible protein 11) Predicted to be involved in negative regulation of cell population proliferation. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TP53I11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 11-44919322-G-A is Benign according to our data. Variant chr11-44919322-G-A is described in ClinVar as [Benign]. Clinvar id is 3057047.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSPAN18	NM_130783.5 linkuse as main transcript	c.432+10G>A		intron_variant		ENST00000520358.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPAN18	ENST00000520358.7 linkuse as main transcript	c.432+10G>A		intron_variant		5	NM_130783.5	P1

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

23982

AN:

151978

Hom.:

2068

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.0448

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.162

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.142

GnomAD3 exomes

AF:

0.144

AC:

36054

AN:

250960

Hom.:

2987

AF XY:

0.142

AC XY:

19232

AN XY:

135662

show subpopulations

Gnomad AFR exome

AF:

0.222

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.153

Gnomad EAS exome

AF:

0.0361

Gnomad SAS exome

AF:

0.163

Gnomad FIN exome

AF:

0.182

Gnomad NFE exome

AF:

0.127

Gnomad OTH exome

AF:

0.142

GnomAD4 exome

AF:

0.131

AC:

190190

AN:

1455886

Hom.:

13291

Cov.:

AF XY:

0.131

AC XY:

95075

AN XY:

724650

show subpopulations

Gnomad4 AFR exome

AF:

0.216

Gnomad4 AMR exome

AF:

0.174

Gnomad4 ASJ exome

AF:

0.147

Gnomad4 EAS exome

AF:

0.0437

Gnomad4 SAS exome

AF:

0.166

Gnomad4 FIN exome

AF:

0.179

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.158

AC:

24002

AN:

152096

Hom.:

2071

Cov.:

AF XY:

0.158

AC XY:

11709

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.222

Gnomad4 AMR

AF:

0.141

Gnomad4 ASJ

AF:

0.150

Gnomad4 EAS

AF:

0.0449

Gnomad4 SAS

AF:

0.158

Gnomad4 FIN

AF:

0.181

Gnomad4 NFE

AF:

0.129

Gnomad4 OTH

AF:

0.141

Alfa

AF:

0.135

Hom.:

1631

Bravo

AF:

0.156

Asia WGS

AF:

0.106

AC:

370

AN:

3478

EpiCase

AF:

0.129

EpiControl

AF:

0.120

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TSPAN18-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 19, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.7

DANN

Benign

0.77

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over