rs1862198

Positions:

• chr5-167876312-G-A
• chr5-167876312-G-C
• chr5-167876312-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395460.1(TENM2):​c.712+117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 829,332 control chromosomes in the GnomAD database, including 280,952 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 0.72 (42613 hom., cov: 31)
  • Exomes 𝑓: 0.83 (238339 hom.)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM2	NM_001395460.1	c.712+117G>A		intron_variant		ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6	c.712+117G>A		intron_variant		5	NM_001395460.1	ENSP00000429430	P1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110157 AN: 151906 Hom.: 42590 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.733

GnomAD4 exome AF: 0.835 AC: 565481 AN: 677308 Hom.: 238339 AF XY: 0.839 AC XY: 294953 AN XY: 351502

Gnomad4 AFR exome AF: 0.413

Gnomad4 AMR exome AF: 0.844

Gnomad4 ASJ exome AF: 0.783

Gnomad4 EAS exome AF: 0.987

Gnomad4 SAS exome AF: 0.904

Gnomad4 FIN exome AF: 0.854

Gnomad4 NFE exome AF: 0.834

Gnomad4 OTH exome AF: 0.803

GnomAD4 genome AF: 0.725 AC: 110215 AN: 152024 Hom.: 42613 Cov.: 31 AF XY: 0.732 AC XY: 54415 AN XY: 74292

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.736

Alfa AF: 0.778 Hom.: 7505

Bravo AF: 0.707

Asia WGS AF: 0.867 AC: 3015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.65
DANN	Benign	0.21

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: rs1862198; hg19: chr5-167303317;