rs11742145

Positions:

• chr5-167405074-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395460.1(TENM2):​c.502+29601T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,120 control chromosomes in the GnomAD database, including 14,436 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 0.42 (14436 hom., cov: 33)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM2	NM_001395460.1	c.502+29601T>C		intron_variant		ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6	c.502+29601T>C		intron_variant		5	NM_001395460.1	ENSP00000429430	P1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63735 AN: 152000 Hom.: 14430 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.419 AC: 63771 AN: 152120 Hom.: 14436 Cov.: 33 AF XY: 0.422 AC XY: 31355 AN XY: 74352

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.407

Alfa AF: 0.470 Hom.: 8692

Bravo AF: 0.408

Asia WGS AF: 0.447 AC: 1552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.35

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: rs11742145; hg19: chr5-166832079;