X-124456849-A-T

Position:

• chrX-124456849-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001163278.2(TENM1):​c.3950-3358T>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 NM_001163278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM1	NM_001163278.2	c.3950-3358T>A		intron_variant			NP_001156750.1
TENM1	NM_001163279.1	c.3947-3358T>A		intron_variant			NP_001156751.1
TENM1	NM_014253.3	c.3929-3358T>A		intron_variant			NP_055068.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM1	ENST00000371130.7	c.3929-3358T>A		intron_variant		1		ENSP00000360171.3
TENM1	ENST00000422452.3	c.3896-3358T>A		intron_variant		1		ENSP00000403954.4
TENM1	ENST00000461429.1	n.383-3358T>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.744 AC: 82121 AN: 110380 Hom.: 22733 Cov.: 23 AF XY: 0.727 AC XY: 23703 AN XY: 32604

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

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.744

Alfa AF: 0.733 Hom.: 6036

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.3
DANN	Benign	0.58

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: rs5910090; hg19: chrX-123590699;