12-71312516-G-T

Variant names:

• chr12-71312516-G-T
• rs7964431
• ENST00000393330.6:c.-275-29697C>A

Variant summary

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

The ENST00000393330.6(TSPAN8):​c.-275-29697C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,112 control chromosomes in the GnomAD database, including 46,923 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 (46923 hom., cov: 32)
• Consequence: TSPAN8 ENST00000393330.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 1 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]

LOC105369832 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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.-275-29697C>A		intron	N/A	ENSP00000377003.2	P19075
	TSPAN8	ENST00000549421.1	TSL:3	n.102+2807C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118846 AN: 151992 Hom.: 46872 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.782 AC: 118954 AN: 152112 Hom.: 46923 Cov.: 32 AF XY: 0.788 AC XY: 58589 AN XY: 74354

African (AFR) AF: 0.863 AC: 35810 AN: 41516

American (AMR) AF: 0.779 AC: 11913 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2329 AN: 3466

East Asian (EAS) AF: 0.991 AC: 5136 AN: 5182

South Asian (SAS) AF: 0.878 AC: 4235 AN: 4822

European-Finnish (FIN) AF: 0.806 AC: 8513 AN: 10560

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48496 AN: 67966

Other (OTH) AF: 0.758 AC: 1600 AN: 2112

Alfa AF: 0.755 Hom.: 5309

Bravo AF: 0.783

Asia WGS AF: 0.901 AC: 3132 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.29
PhyloP100		0.26
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7964431;

hg19: chr12-71706296;