rs10506627

chr12-71272772-T-C

Variant summary

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

The ENST00000393330.6(TSPAN8):c.-110+4579A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 151,926 control chromosomes in the GnomAD database, including 1,287 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 0.12 (1287 hom., cov: 31)
• Consequence: TSPAN8 ENST00000393330.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPAN8	ENST00000393330.6	c.-110+4579A>G		intron_variant		1		P1
TSPAN8	ENST00000549421.1	n.206+9944A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17651 AN: 151808 Hom.: 1286 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.116 AC: 17656 AN: 151926 Hom.: 1287 Cov.: 31 AF XY: 0.124 AC XY: 9205 AN XY: 74246

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.0604

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.0951

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0913 Hom.: 961

Bravo AF: 0.113

Asia WGS AF: 0.161 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.062
Dann	Benign	0.45

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: rs10506627; hg19: chr12-71666552;