rs4760790

Variant names:

• chr12-71241014-A-G
• rs4760790
• ENST00000393330.6:c.-110+36337T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-71241014-A-G
• chr12-71241014-A-T

Variant summary

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

The ENST00000393330.6(TSPAN8):​c.-110+36337T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,042 control chromosomes in the GnomAD database, including 44,398 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 0.76 (44398 hom., cov: 31)
• Consequence: TSPAN8 ENST00000393330.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 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.-110+36337T>C		intron_variant	Intron 4 of 11	1		ENSP00000377003.2
TSPAN8	ENST00000549421.1	n.206+41702T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115600 AN: 151924 Hom.: 44350 Cov.: 31

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.761 AC: 115711 AN: 152042 Hom.: 44398 Cov.: 31 AF XY: 0.761 AC XY: 56593 AN XY: 74332

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.717

Alfa AF: 0.720 Hom.: 46154

Bravo AF: 0.768

Asia WGS AF: 0.747 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.58
DANN	Benign	0.63

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: rs4760790; hg19: chr12-71634794;