chr13-111320927-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152324.3(TEX29):c.37C>A(p.His13Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,611,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152324.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX29 | NM_152324.3 | c.37C>A | p.His13Asn | missense_variant | 2/6 | ENST00000283547.2 | NP_689537.1 | |
TEX29 | XM_017020387.2 | c.118C>A | p.His40Asn | missense_variant | 2/6 | XP_016875876.2 | ||
TEX29 | NM_001303133.1 | c.-40C>A | 5_prime_UTR_variant | 2/7 | NP_001290062.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX29 | ENST00000283547.2 | c.37C>A | p.His13Asn | missense_variant | 2/6 | 1 | NM_152324.3 | ENSP00000283547 | P1 | |
TEX29 | ENST00000497241.5 | c.118C>A | p.His40Asn | missense_variant, NMD_transcript_variant | 2/7 | 5 | ENSP00000431661 |
Frequencies
GnomAD3 genomes AF: 0.0000332 AC: 5AN: 150822Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250564Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135622
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461132Hom.: 0 Cov.: 34 AF XY: 0.0000509 AC XY: 37AN XY: 726864
GnomAD4 genome AF: 0.0000332 AC: 5AN: 150822Hom.: 0 Cov.: 30 AF XY: 0.0000408 AC XY: 3AN XY: 73558
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.37C>A (p.H13N) alteration is located in exon 2 (coding exon 1) of the TEX29 gene. This alteration results from a C to A substitution at nucleotide position 37, causing the histidine (H) at amino acid position 13 to be replaced by an asparagine (N). 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