5-168008989-A-G

Variant names:

• chr5-168008989-A-G
• rs17069578
• NM_001395460.1:c.1186+15807A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001395460.1(TENM2):​c.1186+15807A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,190 control chromosomes in the GnomAD database, including 2,036 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 0.16 (2036 hom., cov: 33)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395460.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM2	NM_001395460.1	MANE Select	c.1186+15807A>G		intron	N/A	NP_001382389.1
	TENM2	NM_001122679.2		c.1186+15807A>G		intron	N/A	NP_001116151.1
	TENM2	NM_001368145.1		c.730+15807A>G		intron	N/A	NP_001355074.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM2	ENST00000518659.6	TSL:5 MANE Select	c.1186+15807A>G		intron	N/A	ENSP00000429430.1
	TENM2	ENST00000520394.5	TSL:1	c.613+15807A>G		intron	N/A	ENSP00000427874.1
	TENM2	ENST00000519204.5	TSL:5	c.823+15807A>G		intron	N/A	ENSP00000428964.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23788 AN: 152072 Hom.: 2032 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.156 AC: 23795 AN: 152190 Hom.: 2036 Cov.: 33 AF XY: 0.153 AC XY: 11376 AN XY: 74396

African (AFR) AF: 0.110 AC: 4566 AN: 41530

American (AMR) AF: 0.261 AC: 3988 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3472

East Asian (EAS) AF: 0.106 AC: 549 AN: 5186

South Asian (SAS) AF: 0.122 AC: 586 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1096 AN: 10600

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11755 AN: 67990

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.180 Hom.: 3371

Bravo AF: 0.170

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	16
DANN	Benign	0.77
PhyloP100		0.29
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: rs17069578; hg19: chr5-167435994;