rs1501802

chr5-167008476-G-Achr5-167008476-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.-190+28953G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,962 control chromosomes in the GnomAD database, including 8,920 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 0.33 (8920 hom., cov: 32)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM2	NM_001395460.1	c.-190+28953G>A		intron_variant		ENST00000518659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM2	ENST00000518659.6	c.-190+28953G>A		intron_variant		5	NM_001395460.1	P1
TENM2	ENST00000695884.1	n.463+28953G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49752 AN: 151844 Hom.: 8919 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.328 AC: 49770 AN: 151962 Hom.: 8920 Cov.: 32 AF XY: 0.332 AC XY: 24629 AN XY: 74242

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.335

Alfa AF: 0.319 Hom.: 1930

Bravo AF: 0.318

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.17
Dann	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1501802; hg19: chr5-166435481;