rs10516045

chr5-168195529-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.2900+234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 149,690 control chromosomes in the GnomAD database, including 126 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 0.024 (126 hom., cov: 30)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM2	NM_001395460.1	c.2900+234T>C		intron_variant		ENST00000518659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM2	ENST00000518659.6	c.2900+234T>C		intron_variant		5	NM_001395460.1	P1

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 3547 AN: 149566 Hom.: 125 Cov.: 30

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0166

Gnomad AMR AF: 0.0539

Gnomad ASJ AF: 0.0224

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.00833

Gnomad MID AF: 0.0194

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0237 AC: 3553 AN: 149690 Hom.: 126 Cov.: 30 AF XY: 0.0245 AC XY: 1785 AN XY: 72930

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.0536

Gnomad4 ASJ AF: 0.0224

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.00833

Gnomad4 NFE AF: 0.0111

Gnomad4 OTH AF: 0.0212

Alfa AF: 0.0152 Hom.: 1

Bravo AF: 0.0292

Asia WGS AF: 0.0830 AC: 287 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.69
Dann	Benign	0.31

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: rs10516045; hg19: chr5-167622534;