chr12-71219496-C-T

Variant names:

• chr12-71219496-C-T
• rs1353362
• ENST00000393330.6:c.-110+57855G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000393330.6(TSPAN8):​c.-110+57855G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 151,682 control chromosomes in the GnomAD database, including 46,819 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 0.78 (46819 hom., cov: 31)
• Consequence: TSPAN8 ENST00000393330.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 19 publications found

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]

LOC105369831 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000393330.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN8	ENST00000393330.6	TSL:1	c.-110+57855G>A		intron	N/A	ENSP00000377003.2	P19075
	TSPAN8	ENST00000549421.1	TSL:3	n.207-61709G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118224 AN: 151564 Hom.: 46760 Cov.: 31

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.780 AC: 118347 AN: 151682 Hom.: 46819 Cov.: 31 AF XY: 0.780 AC XY: 57798 AN XY: 74104

African (AFR) AF: 0.911 AC: 37773 AN: 41454

American (AMR) AF: 0.788 AC: 11962 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2421 AN: 3462

East Asian (EAS) AF: 0.744 AC: 3796 AN: 5102

South Asian (SAS) AF: 0.660 AC: 3178 AN: 4818

European-Finnish (FIN) AF: 0.801 AC: 8475 AN: 10580

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48350 AN: 67768

Other (OTH) AF: 0.731 AC: 1537 AN: 2104

Alfa AF: 0.728 Hom.: 67251

Bravo AF: 0.790

Asia WGS AF: 0.738 AC: 2564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.036
DANN	Benign	0.50
PhyloP100		-1.7
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: rs1353362; hg19: chr12-71613276;