chrX-124939813-A-G

Position:

• chrX-124939813-A-G

Variant summary

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

The ENST00000422452.4(TENM1):​c.217+23724T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 111,984 control chromosomes in the GnomAD database, including 205 homozygotes. There are 1,174 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 0.039 (205 hom., 1174 hem., cov: 23)
• Consequence: TENM1 ENST00000422452.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM1	NM_001163278.2	c.217+23724T>C		intron_variant		ENST00000422452.4	NP_001156750.1
TENM1	XM_017029210.3	c.217+23724T>C		intron_variant			XP_016884699.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM1	ENST00000422452.4	c.217+23724T>C		intron_variant		1	NM_001163278.2	ENSP00000403954	A1
TENM1	ENST00000371130.7	c.217+23724T>C		intron_variant		1		ENSP00000360171	P4

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 4390 AN: 111930 Hom.: 205 Cov.: 23 AF XY: 0.0342 AC XY: 1167 AN XY: 34128

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0203

Gnomad ASJ AF: 0.0166

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00112

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0126

Gnomad NFE AF: 0.00105

Gnomad OTH AF: 0.0299

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

GnomAD4 genome AF: 0.0392 AC: 4394 AN: 111984 Hom.: 205 Cov.: 23 AF XY: 0.0343 AC XY: 1174 AN XY: 34192

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0202

Gnomad4 ASJ AF: 0.0166

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00112

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00105

Gnomad4 OTH AF: 0.0295

Alfa AF: 0.00724 Hom.: 201

Bravo AF: 0.0466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.4
DANN	Benign	0.81

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: rs7060947; hg19: chrX-124073662;