5-168062044-CTTT-CTTTTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001395460.1(TENM2):c.1310-5_1310-4dup variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.085 (662 hom., cov: 0)
  • Exomes 𝑓: 0.11 (434 hom.)
• Consequence: TENM2 NM_001395460.1 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.806

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 -10 ACMG points.

• BP6: Variant 5-168062044-C-CTT is Benign according to our data. Variant chr5-168062044-C-CTT is described in ClinVar as [Benign]. Clinvar id is 403528.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM2	NM_001395460.1	c.1310-5_1310-4dup		splice_polypyrimidine_tract_variant, intron_variant		ENST00000518659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM2	ENST00000518659.6	c.1310-5_1310-4dup		splice_polypyrimidine_tract_variant, intron_variant		5	NM_001395460.1	P1

Frequencies

GnomAD3 genomes AF: 0.0855 AC: 12563 AN: 147002 Hom.: 664 Cov.: 0

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.0815

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.00256

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.116

GnomAD4 exome AF: 0.108 AC: 140929 AN: 1302388 Hom.: 434 Cov.: 0 AF XY: 0.109 AC XY: 70613 AN XY: 647566

Gnomad4 AFR exome AF: 0.0329

Gnomad4 AMR exome AF: 0.0523

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.00164

Gnomad4 SAS exome AF: 0.134

Gnomad4 FIN exome AF: 0.0894

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.105

GnomAD4 genome AF: 0.0854 AC: 12552 AN: 147052 Hom.: 662 Cov.: 0 AF XY: 0.0863 AC XY: 6157 AN XY: 71332

Gnomad4 AFR AF: 0.0363

Gnomad4 AMR AF: 0.0929

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.00256

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0964

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.114

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 8.2% of total chromosomes in ExAC -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11411759; hg19: chr5-167489049;