chr5-167704322-T-C

Variant names:

• chr5-167704322-T-C
• rs10516037
• NM_001395460.1:c.503-171664T>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.503-171664T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 152,174 control chromosomes in the GnomAD database, including 645 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 0.062 (645 hom., cov: 32)
• Consequence: TENM2 NM_001395460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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.503-171664T>C		intron	N/A	NP_001382389.1
	TENM2	NM_001122679.2		c.503-171664T>C		intron	N/A	NP_001116151.1
	TENM2	NM_001368145.1		c.46+130296T>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.503-171664T>C		intron	N/A	ENSP00000429430.1
	TENM2	ENST00000695886.1		c.46+130296T>C		intron	N/A	ENSP00000512239.1
	TENM2	ENST00000695885.1		n.46+130296T>C		intron	N/A	ENSP00000512238.1

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9423 AN: 152054 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0621 AC: 9453 AN: 152174 Hom.: 645 Cov.: 32 AF XY: 0.0649 AC XY: 4828 AN XY: 74400

African (AFR) AF: 0.0846 AC: 3512 AN: 41510

American (AMR) AF: 0.138 AC: 2112 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0162 AC: 56 AN: 3466

East Asian (EAS) AF: 0.305 AC: 1571 AN: 5144

South Asian (SAS) AF: 0.0970 AC: 468 AN: 4824

European-Finnish (FIN) AF: 0.0102 AC: 108 AN: 10608

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.0220 AC: 1499 AN: 68010

Other (OTH) AF: 0.0530 AC: 112 AN: 2112

Alfa AF: 0.0361 Hom.: 90

Bravo AF: 0.0729

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.42
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: rs10516037; hg19: chr5-167131327;