5-167762607-T-C

Variant names:

• chr5-167762607-T-C
• rs10516038
• NM_001395460.1:c.503-113379T>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.503-113379T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,118 control chromosomes in the GnomAD database, including 28,694 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 0.59 (28694 hom., cov: 33)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.57
• Publications: 5 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 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.503-113379T>C		intron	N/A	NP_001382389.1
	TENM2	NM_001122679.2		c.503-113379T>C		intron	N/A	NP_001116151.1
	TENM2	NM_001368145.1		c.47-113379T>C		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.503-113379T>C		intron	N/A	ENSP00000429430.1
	TENM2	ENST00000520394.5	TSL:1	c.139+7415T>C		intron	N/A	ENSP00000427874.1
	TENM2	ENST00000519204.5	TSL:5	c.139+7415T>C		intron	N/A	ENSP00000428964.1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89925 AN: 152000 Hom.: 28696 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.591 AC: 89935 AN: 152118 Hom.: 28694 Cov.: 33 AF XY: 0.585 AC XY: 43481 AN XY: 74352

African (AFR) AF: 0.369 AC: 15326 AN: 41510

American (AMR) AF: 0.535 AC: 8162 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2545 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1968 AN: 5162

South Asian (SAS) AF: 0.630 AC: 3033 AN: 4816

European-Finnish (FIN) AF: 0.666 AC: 7040 AN: 10576

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49781 AN: 68008

Other (OTH) AF: 0.637 AC: 1348 AN: 2116

Alfa AF: 0.654 Hom.: 10560

Bravo AF: 0.570

Asia WGS AF: 0.489 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.13
DANN	Benign	0.61
PhyloP100		-3.6
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: rs10516038; hg19: chr5-167189612;