X-124383680-A-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The ENST00000422452.4(TENM1):c.7251T>G(p.Asn2417Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,207,930 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000036 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.000010 ( 0 hom. 3 hem. )
Consequence
TENM1
ENST00000422452.4 missense
ENST00000422452.4 missense
Scores
3
9
5
Clinical Significance
Conservation
PhyloP100: 0.929
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]
STAG2 (HGNC:11355): (STAG2 cohesin complex component) The protein encoded by this gene is a subunit of the cohesin complex, which regulates the separation of sister chromatids during cell division. Targeted inactivation of this gene results in chromatid cohesion defects and aneuploidy, suggesting that genetic disruption of cohesin is a cause of aneuploidy in human cancer. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, TENM1
BS2
?
High Hemizygotes in GnomAdExome at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM1 | NM_001163278.2 | c.7251T>G | p.Asn2417Lys | missense_variant | 33/35 | ENST00000422452.4 | |
TENM1 | XM_017029210.3 | c.7350T>G | p.Asn2450Lys | missense_variant | 33/35 | ||
LOC105373331 | XR_938576.1 | n.88+2686A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM1 | ENST00000422452.4 | c.7251T>G | p.Asn2417Lys | missense_variant | 33/35 | 1 | NM_001163278.2 | A1 | |
TENM1 | ENST00000371130.7 | c.7230T>G | p.Asn2410Lys | missense_variant | 29/31 | 1 | P4 | ||
STAG2 | ENST00000469481.1 | n.454-28142A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000357 AC: 4AN: 111946Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34124
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000823 AC: 15AN: 182356Hom.: 0 AF XY: 0.000119 AC XY: 8AN XY: 66952
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GnomAD4 exome AF: 0.0000100 AC: 11AN: 1095984Hom.: 0 Cov.: 30 AF XY: 0.00000830 AC XY: 3AN XY: 361416
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.7251T>G (p.N2417K) alteration is located in exon 30 (coding exon 30) of the TENM1 gene. This alteration results from a T to G substitution at nucleotide position 7251, causing the asparagine (N) at amino acid position 2417 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Pathogenic
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Gain of ubiquitination at N2410 (P = 0.0185);.;
MVP
MPC
0.82
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at