rs11178748

Variant names:

• chr12-71341747-G-A
• rs11178748
• ENST00000393330.6:c.-275-58928C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-71341747-G-A
• chr12-71341747-G-T

Variant summary

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

The ENST00000393330.6(TSPAN8):​c.-275-58928C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 152,086 control chromosomes in the GnomAD database, including 1,113 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 0.097 (1113 hom., cov: 32)
• Consequence: TSPAN8 ENST00000393330.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

TSPAN8 (HGNC:11855): (tetraspanin 8) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. This gene is expressed in different carcinomas. The use of alternate polyadenylation sites has been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPAN8	ENST00000393330.6	c.-275-58928C>T		intron_variant	Intron 2 of 11	1		ENSP00000377003.2

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14768 AN: 151968 Hom.: 1110 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.0415

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.0891

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

GnomAD4 genome AF: 0.0972 AC: 14787 AN: 152086 Hom.: 1113 Cov.: 32 AF XY: 0.0942 AC XY: 7006 AN XY: 74346

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0631

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0546

Gnomad4 OTH AF: 0.0877

Alfa AF: 0.0583 Hom.: 361

Bravo AF: 0.103

Asia WGS AF: 0.0380 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.35

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: rs11178748; hg19: chr12-71735527;