5-168062044-CTTT-CTT

Variant names:

• chr5-168062044-CT-C
• rs11411759
• NM_001395460.1:c.1310-4delT

Variant summary

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

The NM_001395460.1(TENM2):​c.1310-4delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (4739 hom., cov: 0)
  • Exomes 𝑓: 0.23 (13185 hom.)
• Consequence: TENM2 NM_001395460.1 splice_region, 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 (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM2	NM_001395460.1	c.1310-4delT		splice_region_variant, intron_variant	Intron 8 of 30	ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6	c.1310-15delT		intron_variant	Intron 8 of 30	5	NM_001395460.1	ENSP00000429430.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 36154 AN: 146920 Hom.: 4727 Cov.: 0

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.226 AC: 293538 AN: 1300740 Hom.: 13185 Cov.: 0 AF XY: 0.228 AC XY: 147249 AN XY: 646646

Gnomad4 AFR exome AF: 0.321

Gnomad4 AMR exome AF: 0.193

Gnomad4 ASJ exome AF: 0.230

Gnomad4 EAS exome AF: 0.404

Gnomad4 SAS exome AF: 0.311

Gnomad4 FIN exome AF: 0.227

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.240

GnomAD4 genome AF: 0.246 AC: 36190 AN: 146968 Hom.: 4739 Cov.: 0 AF XY: 0.246 AC XY: 17536 AN XY: 71294

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.232

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;