chr5-167762607-T-C

Position:

• chr5-167762607-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM2	NM_001395460.1	c.503-113379T>C		intron_variant		ENST00000518659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM2	ENST00000518659.6	c.503-113379T>C		intron_variant		5	NM_001395460.1	P1

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.637

Alfa AF: 0.635 Hom.: 6150

Bravo AF: 0.570

Asia WGS AF: 0.489 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.13
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516038; hg19: chr5-167189612;