rs10516045

Variant names:

• chr5-168195529-T-C
• rs10516045
• NM_001395460.1:c.2900+234T>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.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
• Publications: 1 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=-0.88).
• 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 rank	MANE	Protein	UniProt
TENM2	NM_001395460.1	c.2900+234T>C		intron_variant	Intron 17 of 30	ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6	c.2900+234T>C		intron_variant	Intron 17 of 30	5	NM_001395460.1	ENSP00000429430.1

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

African (AFR) AF: 0.0191 AC: 773 AN: 40552

American (AMR) AF: 0.0536 AC: 806 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.0224 AC: 77 AN: 3438

East Asian (EAS) AF: 0.188 AC: 938 AN: 4984

South Asian (SAS) AF: 0.0133 AC: 62 AN: 4666

European-Finnish (FIN) AF: 0.00833 AC: 85 AN: 10206

Middle Eastern (MID) AF: 0.0174 AC: 5 AN: 288

European-Non Finnish (NFE) AF: 0.0111 AC: 748 AN: 67554

Other (OTH) AF: 0.0212 AC: 44 AN: 2074

Alfa AF: 0.0190 Hom.: 144

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
PhyloP100		-1.4
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: rs10516045; hg19: chr5-167622534;