rs2066918

chrX-125058599-C-A

Variant summary

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

The ENST00000422452.4(TENM1):c.-64-94782G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 109,841 control chromosomes in the GnomAD database, including 6,864 homozygotes. There are 10,902 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 0.35 (6864 hom., 10902 hem., cov: 22)
• Consequence: TENM1 ENST00000422452.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.919

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM1	NM_001163278.2	c.-64-94782G>T		intron_variant		ENST00000422452.4
TENM1	XM_017029210.3	c.-64-94782G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM1	ENST00000422452.4	c.-64-94782G>T		intron_variant		1	NM_001163278.2	A1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 38360 AN: 109785 Hom.: 6860 Cov.: 22 AF XY: 0.337 AC XY: 10853 AN XY: 32181

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.350 AC: 38418 AN: 109841 Hom.: 6864 Cov.: 22 AF XY: 0.338 AC XY: 10902 AN XY: 32247

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.324

Alfa AF: 0.218 Hom.: 12967

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.7
Dann	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2066918; hg19: chrX-124192448;