ENST00000371130.7:c.3929-3358T>A

Variant names:

• chrX-124456849-A-T
• rs5910090
• NM_001163278.2:c.3950-3358T>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000371130.7(TENM1):​c.3929-3358T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.74 (22735 hom., 23769 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: TENM1 ENST00000371130.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 0 publications found

Genes affected

TENM1 (HGNC:8117): (teneurin transmembrane protein 1) The protein encoded by this gene belongs to the tenascin family and teneurin subfamily. It is expressed in the neurons and may function as a cellular signal transducer. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

TENM1 Gene-Disease associations (from GenCC):

• isolated congenital anosmia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• anosmia

  Inheritance: XL Classification: LIMITED Submitted by: Ambry Genetics
• cerebral palsy

  Inheritance: XL Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371130.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM1	NM_001163278.2	MANE Select	c.3950-3358T>A		intron	N/A	NP_001156750.1	Q9UKZ4-2
	TENM1	NM_001163279.1		c.3947-3358T>A		intron	N/A	NP_001156751.1	B7ZMH4
	TENM1	NM_014253.3		c.3929-3358T>A		intron	N/A	NP_055068.2	Q9UKZ4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM1	ENST00000422452.4	TSL:1 MANE Select	c.3950-3358T>A		intron	N/A	ENSP00000403954.4	Q9UKZ4-2
	TENM1	ENST00000371130.7	TSL:1	c.3929-3358T>A		intron	N/A	ENSP00000360171.3	Q9UKZ4-1
	TENM1	ENST00000461429.1	TSL:3	n.383-3358T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.744 AC: 82121 AN: 110380 Hom.: 22733 Cov.: 23

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.749

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.741

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.744 AC: 82187 AN: 110432 Hom.: 22735 Cov.: 23 AF XY: 0.728 AC XY: 23769 AN XY: 32666

African (AFR) AF: 0.918 AC: 27845 AN: 30327

American (AMR) AF: 0.702 AC: 7302 AN: 10401

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 1992 AN: 2634

East Asian (EAS) AF: 0.193 AC: 677 AN: 3509

South Asian (SAS) AF: 0.540 AC: 1411 AN: 2611

European-Finnish (FIN) AF: 0.670 AC: 3890 AN: 5803

Middle Eastern (MID) AF: 0.757 AC: 162 AN: 214

European-Non Finnish (NFE) AF: 0.709 AC: 37404 AN: 52749

Other (OTH) AF: 0.744 AC: 1125 AN: 1513

Alfa AF: 0.733 Hom.: 6036

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.3
DANN	Benign	0.58
PhyloP100		0.50
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: rs5910090; hg19: chrX-123590699;