5-168062044-CTTT-CTT

Variant names:

• chr5-168062044-CT-C
• rs11411759
• NM_001395460.1:c.1310-4delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001395460.1(TENM2):​c.1310-4delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.25 (4739 hom., cov: 0)
  • Exomes 𝑓: 0.23 (13185 hom.)
• Consequence: TENM2 NM_001395460.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806
• 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM2	NM_001395460.1	MANE Select	c.1310-4delT		splice_region intron	N/A	NP_001382389.1	Q9NT68-1
	TENM2	NM_001122679.2		c.1310-4delT		splice_region intron	N/A	NP_001116151.1
	TENM2	NM_001368145.1		c.854-4delT		splice_region intron	N/A	NP_001355074.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM2	ENST00000518659.6	TSL:5 MANE Select	c.1310-15delT		intron	N/A	ENSP00000429430.1	Q9NT68-1
	TENM2	ENST00000520394.5	TSL:1	c.614-15delT		intron	N/A	ENSP00000427874.1	F8VNQ3
	TENM2	ENST00000519204.5	TSL:5	c.947-15delT		intron	N/A	ENSP00000428964.1	G3V106

Frequencies

GnomAD3 genomes AF: 0.246 AC: 36154 AN: 146920 Hom.: 4727 Cov.: 0

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.224

GnomAD2 exomes AF: 0.264 AC: 45396 AN: 172048 AF XY: 0.264

Gnomad AFR exome AF: 0.344

Gnomad AMR exome AF: 0.222

Gnomad ASJ exome AF: 0.236

Gnomad EAS exome AF: 0.433

Gnomad FIN exome AF: 0.237

Gnomad NFE exome AF: 0.231

Gnomad OTH exome AF: 0.243

GnomAD4 exome AF: 0.226 AC: 293538 AN: 1300740 Hom.: 13185 Cov.: 0 AF XY: 0.228 AC XY: 147249 AN XY: 646646

African (AFR) AF: 0.321 AC: 9150 AN: 28488

American (AMR) AF: 0.193 AC: 6836 AN: 35342

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 5375 AN: 23386

East Asian (EAS) AF: 0.404 AC: 13572 AN: 33616

South Asian (SAS) AF: 0.311 AC: 23497 AN: 75526

European-Finnish (FIN) AF: 0.227 AC: 10619 AN: 46704

Middle Eastern (MID) AF: 0.240 AC: 912 AN: 3800

European-Non Finnish (NFE) AF: 0.211 AC: 210665 AN: 1000098

Other (OTH) AF: 0.240 AC: 12912 AN: 53780

GnomAD4 genome AF: 0.246 AC: 36190 AN: 146968 Hom.: 4739 Cov.: 0 AF XY: 0.246 AC XY: 17536 AN XY: 71294

African (AFR) AF: 0.309 AC: 12427 AN: 40166

American (AMR) AF: 0.151 AC: 2233 AN: 14776

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 792 AN: 3454

East Asian (EAS) AF: 0.449 AC: 2277 AN: 5066

South Asian (SAS) AF: 0.344 AC: 1603 AN: 4666

European-Finnish (FIN) AF: 0.227 AC: 1992 AN: 8786

Middle Eastern (MID) AF: 0.254 AC: 72 AN: 284

European-Non Finnish (NFE) AF: 0.209 AC: 13950 AN: 66834

Other (OTH) AF: 0.232 AC: 471 AN: 2028

Alfa AF: 0.209 Hom.: 100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.81
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: rs11411759; hg19: chr5-167489049; COSMIC: COSV69140793;