11-44915127-C-T

Position:

• chr11-44915127-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130783.5(TSPAN18):​c.259-2845C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,046 control chromosomes in the GnomAD database, including 23,207 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 0.55 (23207 hom., cov: 33)
• Consequence: TSPAN18 NM_130783.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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]

TSPAN18 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSPAN18	NM_130783.5	c.259-2845C>T		intron_variant		ENST00000520358.7	NP_570139.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSPAN18	ENST00000520358.7	c.259-2845C>T		intron_variant		5	NM_130783.5	ENSP00000429993.2

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83130 AN: 151928 Hom.: 23184 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.547 AC: 83200 AN: 152046 Hom.: 23207 Cov.: 33 AF XY: 0.554 AC XY: 41197 AN XY: 74340

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.534

Alfa AF: 0.425 Hom.: 1467

Bravo AF: 0.552

Asia WGS AF: 0.766 AC: 2662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.56

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

Other links and lift over

dbSNP: rs1867791; hg19: chr11-44936678;