5-168177231-G-C

Variant names:

• chr5-168177231-G-C
• rs10516044
• NM_001395460.1:c.2570-13106G>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.2570-13106G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0836 in 152,314 control chromosomes in the GnomAD database, including 669 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 0.084 (669 hom., cov: 33)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 1 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]

ENSG00000253925 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 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.2570-13106G>C		intron	N/A	NP_001382389.1
	TENM2	NM_001122679.2		c.2543-13106G>C		intron	N/A	NP_001116151.1
	TENM2	NM_001368145.1		c.2114-13106G>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.2570-13106G>C		intron	N/A	ENSP00000429430.1
	TENM2	ENST00000520394.5	TSL:1	c.1874-13106G>C		intron	N/A	ENSP00000427874.1
	TENM2	ENST00000519204.5	TSL:5	c.2207-13106G>C		intron	N/A	ENSP00000428964.1

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12753 AN: 152196 Hom.: 672 Cov.: 33

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0812

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0862

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0836 AC: 12740 AN: 152314 Hom.: 669 Cov.: 33 AF XY: 0.0825 AC XY: 6146 AN XY: 74476

African (AFR) AF: 0.0207 AC: 860 AN: 41582

American (AMR) AF: 0.0808 AC: 1236 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 418 AN: 3472

East Asian (EAS) AF: 0.0862 AC: 447 AN: 5184

South Asian (SAS) AF: 0.122 AC: 588 AN: 4830

European-Finnish (FIN) AF: 0.0877 AC: 930 AN: 10610

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7930 AN: 68024

Other (OTH) AF: 0.107 AC: 226 AN: 2110

Alfa AF: 0.0433 Hom.: 44

Bravo AF: 0.0792

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.74
PhyloP100		0.079
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: rs10516044; hg19: chr5-167604236;