NM_005725.6:c.69+7581T>A

Variant names:

• chr1-115081783-A-T
• rs910623
• NM_005725.6:c.69+7581T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005725.6(TSPAN2):​c.69+7581T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TSPAN2 NM_005725.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876
• Publications: 6 publications found

Genes affected

TSPAN2 (HGNC:20659): (tetraspanin 2) 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. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSPAN2	NM_005725.6	c.69+7581T>A		intron_variant	Intron 1 of 7	ENST00000369516.7	NP_005716.2
TSPAN2	NM_001308315.2	c.69+7581T>A		intron_variant	Intron 1 of 6		NP_001295244.1
TSPAN2	NM_001308316.2	c.69+7581T>A		intron_variant	Intron 1 of 6		NP_001295245.1
TSPAN2	XM_016999996.2	c.69+7581T>A		intron_variant	Intron 1 of 5		XP_016855485.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPAN2	ENST00000369516.7	c.69+7581T>A		intron_variant	Intron 1 of 7	1	NM_005725.6	ENSP00000358529.2
TSPAN2	ENST00000433172.3	c.51+7581T>A		intron_variant	Intron 1 of 6	1		ENSP00000415256.1
TSPAN2	ENST00000369515.6	c.69+7581T>A		intron_variant	Intron 1 of 6	3		ENSP00000358528.2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.80
PhyloP100		0.88

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: rs910623; hg19: chr1-115624404;