5-168177231-G-C

Variant summary

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

The NM_001395460.1(TENM2):c.2570-13106G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0836 in 152,314 control chromosomes in the GnomAD database, including 669 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 0.084 (669 hom., cov: 33)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM2	NM_001395460.1	c.2570-13106G>C		intron_variant		ENST00000518659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM2	ENST00000518659.6	c.2570-13106G>C		intron_variant		5	NM_001395460.1	P1
	ENST00000517408.1	n.1673+7904C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12753 AN: 152196 Hom.: 672 Cov.: 33

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0812

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0862

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0836 AC: 12740 AN: 152314 Hom.: 669 Cov.: 33 AF XY: 0.0825 AC XY: 6146 AN XY: 74476

Gnomad4 AFR AF: 0.0207

Gnomad4 AMR AF: 0.0808

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0862

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0877

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0433 Hom.: 44

Bravo AF: 0.0792

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.8
Dann	Benign	0.74

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: rs10516044; hg19: chr5-167604236;