rs10521726

Positions:

• chrX-124533371-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000371130.7(TENM1):​c.2652-3388C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0823 in 111,288 control chromosomes in the GnomAD database, including 271 homozygotes. There are 2,696 hemizygotes in GnomAD. 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 0.082 (271 hom., 2696 hem., cov: 22)
• Consequence: TENM1 ENST00000371130.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM1	NM_001163278.2	c.2652-3388C>T		intron_variant		ENST00000422452.4
TENM1	XM_017029210.3	c.2652-3388C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM1	ENST00000422452.4	c.2652-3388C>T		intron_variant		1	NM_001163278.2	A1
TENM1	ENST00000371130.7	c.2652-3388C>T		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 9149 AN: 111232 Hom.: 270 Cov.: 22 AF XY: 0.0801 AC XY: 2682 AN XY: 33488

Gnomad AFR AF: 0.0780

Gnomad AMI AF: 0.0146

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.0888

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

GnomAD4 genome AF: 0.0823 AC: 9159 AN: 111288 Hom.: 271 Cov.: 22 AF XY: 0.0803 AC XY: 2696 AN XY: 33554

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0843

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0885 Hom.: 3744

Bravo AF: 0.0788

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.50

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: rs10521726; hg19: chrX-123667221;