5-167439431-C-T

Variant names:

• chr5-167439431-C-T
• rs6887079
• NM_001395460.1:c.502+63958C>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.502+63958C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,948 control chromosomes in the GnomAD database, including 22,211 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 0.54 (22211 hom., cov: 31)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM2	NM_001395460.1	c.502+63958C>T		intron_variant	Intron 4 of 30	ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6	c.502+63958C>T		intron_variant	Intron 4 of 30	5	NM_001395460.1	ENSP00000429430.1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81562 AN: 151832 Hom.: 22208 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.537 AC: 81605 AN: 151948 Hom.: 22211 Cov.: 31 AF XY: 0.535 AC XY: 39749 AN XY: 74262

African (AFR) AF: 0.622 AC: 25781 AN: 41428

American (AMR) AF: 0.488 AC: 7451 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3343 AN: 5144

South Asian (SAS) AF: 0.628 AC: 3026 AN: 4816

European-Finnish (FIN) AF: 0.482 AC: 5080 AN: 10532

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33844 AN: 67970

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.513 Hom.: 57634

Bravo AF: 0.539

Asia WGS AF: 0.598 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.52
PhyloP100		0.19
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: rs6887079; hg19: chr5-166866436;