11-44915127-C-T

Variant names:

• chr11-44915127-C-T
• rs1867791
• NM_130783.5:c.259-2845C>T

Variant summary

Our verdict is Benign. The variant received -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
• 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]

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130783.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN18	NM_130783.5	MANE Select	c.259-2845C>T		intron	N/A	NP_570139.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN18	ENST00000520358.7	TSL:5 MANE Select	c.259-2845C>T		intron	N/A	ENSP00000429993.2	Q96SJ8
	TSPAN18	ENST00000518429.2	TSL:1	c.268-2845C>T		intron	N/A	ENSP00000429020.2	H0YB98
	TP53I11	ENST00000354556.8	TSL:1	n.335-11237G>A		intron	N/A	ENSP00000346564.4	E9PPM1

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

African (AFR) AF: 0.565 AC: 23431 AN: 41470

American (AMR) AF: 0.619 AC: 9446 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3468

East Asian (EAS) AF: 0.831 AC: 4286 AN: 5156

South Asian (SAS) AF: 0.724 AC: 3492 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5649 AN: 10566

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33761 AN: 67978

Other (OTH) AF: 0.534 AC: 1126 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.56
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: rs1867791; hg19: chr11-44936678;