rs1894516

Positions:

• chrX-124999772-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000422452.4(TENM1):​c.-64-35955C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 109,815 control chromosomes in the GnomAD database, including 8,155 homozygotes. There are 13,036 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 0.42 (8155 hom., 13036 hem., cov: 22)
• Consequence: TENM1 ENST00000422452.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM1	NM_001163278.2	c.-64-35955C>T		intron_variant		ENST00000422452.4	NP_001156750.1
TENM1	XM_017029210.3	c.-64-35955C>T		intron_variant			XP_016884699.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM1	ENST00000422452.4	c.-64-35955C>T		intron_variant		1	NM_001163278.2	ENSP00000403954	A1

Frequencies

GnomAD3 genomes AF: 0.417 AC: 45824 AN: 109767 Hom.: 8154 Cov.: 22 AF XY: 0.403 AC XY: 12992 AN XY: 32215

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.418 AC: 45863 AN: 109815 Hom.: 8155 Cov.: 22 AF XY: 0.404 AC XY: 13036 AN XY: 32273

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.385

Alfa AF: 0.354 Hom.: 7545

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	7.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1894516; hg19: chrX-124133621;