rs1422930

Variant names:

• chr5-167970588-C-T
• rs1422930
• NM_001395460.1:c.947+17766C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395460.1(TENM2):​c.947+17766C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,022 control chromosomes in the GnomAD database, including 10,659 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 0.34 (10659 hom., cov: 32)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM2	NM_001395460.1	c.947+17766C>T		intron_variant	Intron 6 of 30	ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6	c.947+17766C>T		intron_variant	Intron 6 of 30	5	NM_001395460.1	ENSP00000429430.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51519 AN: 151906 Hom.: 10633 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.339 AC: 51598 AN: 152022 Hom.: 10659 Cov.: 32 AF XY: 0.346 AC XY: 25691 AN XY: 74326

African (AFR) AF: 0.517 AC: 21429 AN: 41426

American (AMR) AF: 0.440 AC: 6729 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 633 AN: 3468

East Asian (EAS) AF: 0.668 AC: 3444 AN: 5152

South Asian (SAS) AF: 0.452 AC: 2172 AN: 4810

European-Finnish (FIN) AF: 0.212 AC: 2242 AN: 10578

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14115 AN: 67976

Other (OTH) AF: 0.318 AC: 671 AN: 2112

Alfa AF: 0.286 Hom.: 1012

Bravo AF: 0.367

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.75
PhyloP100		0.033
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: rs1422930; hg19: chr5-167397593;