Menu
GeneBe

11-44926712-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_130783.5(TSPAN18):c.654C>T(p.Tyr218=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00378 in 1,614,132 control chromosomes in the GnomAD database, including 210 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 105 hom., cov: 33)
Exomes 𝑓: 0.0020 ( 105 hom. )

Consequence

TSPAN18
NM_130783.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.392
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]
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-44926712-C-T is Benign according to our data. Variant chr11-44926712-C-T is described in ClinVar as [Benign]. Clinvar id is 768442.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.392 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0697 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TSPAN18NM_130783.5 linkuse as main transcriptc.654C>T p.Tyr218= synonymous_variant 9/10 ENST00000520358.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TSPAN18ENST00000520358.7 linkuse as main transcriptc.654C>T p.Tyr218= synonymous_variant 9/105 NM_130783.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0204
AC:
3109
AN:
152174
Hom.:
104
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0719
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00582
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.0134
GnomAD3 exomes
AF:
0.00518
AC:
1303
AN:
251446
Hom.:
51
AF XY:
0.00352
AC XY:
479
AN XY:
135898
show subpopulations
Gnomad AFR exome
AF:
0.0724
Gnomad AMR exome
AF:
0.00249
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000167
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00204
AC:
2982
AN:
1461840
Hom.:
105
Cov.:
30
AF XY:
0.00175
AC XY:
1276
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.0735
Gnomad4 AMR exome
AF:
0.00318
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000128
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000962
Gnomad4 OTH exome
AF:
0.00414
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0204
AC:
3114
AN:
152292
Hom.:
105
Cov.:
33
AF XY:
0.0197
AC XY:
1465
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.0718
Gnomad4 AMR
AF:
0.00581
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.0132
Alfa
AF:
0.00943
Hom.:
21
Bravo
AF:
0.0228
Asia WGS
AF:
0.00491
AC:
18
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.000237

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeOct 09, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
Cadd
Benign
7.6
Dann
Benign
0.78

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.

Other links and lift over

dbSNP: rs34695714; hg19: chr11-44948263; API