rs11742145

Variant names:

• chr5-167405074-T-C
• rs11742145
• NM_001395460.1:c.502+29601T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395460.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM2	NM_001395460.1	MANE Select	c.502+29601T>C		intron	N/A	NP_001382389.1
	TENM2	NM_001122679.2		c.502+29601T>C		intron	N/A	NP_001116151.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM2	ENST00000518659.6	TSL:5 MANE Select	c.502+29601T>C		intron	N/A	ENSP00000429430.1

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

African (AFR) AF: 0.238 AC: 9882 AN: 41534

American (AMR) AF: 0.487 AC: 7429 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3472

East Asian (EAS) AF: 0.463 AC: 2386 AN: 5158

South Asian (SAS) AF: 0.407 AC: 1965 AN: 4830

European-Finnish (FIN) AF: 0.533 AC: 5634 AN: 10580

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.491 AC: 33374 AN: 67984

Other (OTH) AF: 0.407 AC: 858 AN: 2108

Alfa AF: 0.469 Hom.: 9628

Bravo AF: 0.408

Asia WGS AF: 0.447 AC: 1552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.35
PhyloP100		-0.36
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

Other links and lift over

dbSNP: rs11742145; hg19: chr5-166832079;