5-167284988-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_001395460.1(TENM2):c.151C>T(p.His51Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000322 in 1,551,902 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H51R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001395460.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM2 | NM_001395460.1 | c.151C>T | p.His51Tyr | missense_variant | 3/31 | ENST00000518659.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM2 | ENST00000518659.6 | c.151C>T | p.His51Tyr | missense_variant | 3/31 | 5 | NM_001395460.1 | P1 | |
TENM2 | ENST00000695884.1 | n.803C>T | non_coding_transcript_exon_variant | 3/4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000127 AC: 2AN: 157846Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 83330
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1399690Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 690334
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2023 | The c.151C>T (p.H51Y) alteration is located in exon 1 (coding exon 1) of the TENM2 gene. This alteration results from a C to T substitution at nucleotide position 151, causing the histidine (H) at amino acid position 51 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at