5-168062044-CTTT-CTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001395460.1(TENM2):c.1310-4dup variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.39 (11650 hom., cov: 0)
  • Exomes 𝑓: 0.35 (9804 hom.)
  • Failed GnomAD Quality Control
• Consequence: TENM2 NM_001395460.1 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806

Genes affected

TENM2 (HGNC:29943): (teneurin transmembrane protein 2) Enables cell adhesion molecule binding activity and signaling receptor binding activity. Involved in several processes, including calcium-mediated signaling using intracellular calcium source; heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules; and retrograde trans-synaptic signaling by trans-synaptic protein complex. Located in cell-cell junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM2	NM_001395460.1	c.1310-4dup		splice_polypyrimidine_tract_variant, intron_variant		ENST00000518659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM2	ENST00000518659.6	c.1310-4dup		splice_polypyrimidine_tract_variant, intron_variant		5	NM_001395460.1	P1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 57200 AN: 146910 Hom.: 11656 Cov.: 0

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.368

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.354 AC: 463598 AN: 1310586 Hom.: 9804 Cov.: 0 AF XY: 0.351 AC XY: 228359 AN XY: 651188

Gnomad4 AFR exome AF: 0.243

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.325

Gnomad4 EAS exome AF: 0.187

Gnomad4 SAS exome AF: 0.252

Gnomad4 FIN exome AF: 0.383

Gnomad4 NFE exome AF: 0.374

Gnomad4 OTH exome AF: 0.337

GnomAD4 genome AF: 0.389 AC: 57190 AN: 146960 Hom.: 11650 Cov.: 0 AF XY: 0.387 AC XY: 27616 AN XY: 71278

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11411759; hg19: chr5-167489049;