X-105220384-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_031274.5(TEX13A):c.14C>G(p.Pro5Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 1,185,313 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031274.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEX13A | NM_031274.5 | c.14C>G | p.Pro5Arg | missense_variant | 2/3 | ENST00000600991.6 | |
IL1RAPL2 | NM_017416.2 | c.357-13434G>C | intron_variant | ENST00000372582.6 | |||
TEX13A | NM_001291277.2 | c.14C>G | p.Pro5Arg | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX13A | ENST00000600991.6 | c.14C>G | p.Pro5Arg | missense_variant | 2/3 | 1 | NM_031274.5 | P1 | |
TEX13A | ENST00000609007.3 | c.14C>G | p.Pro5Arg | missense_variant | 2/3 | 1 | P1 | ||
IL1RAPL2 | ENST00000372582.6 | c.357-13434G>C | intron_variant | 1 | NM_017416.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000108 AC: 12AN: 111438Hom.: 0 Cov.: 22 AF XY: 0.0000595 AC XY: 2AN XY: 33626
GnomAD4 exome AF: 0.00000559 AC: 6AN: 1073875Hom.: 0 Cov.: 31 AF XY: 0.00000577 AC XY: 2AN XY: 346529
GnomAD4 genome ? AF: 0.000108 AC: 12AN: 111438Hom.: 0 Cov.: 22 AF XY: 0.0000595 AC XY: 2AN XY: 33626
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2024 | The c.14C>G (p.P5R) alteration is located in exon 2 (coding exon 1) of the TEX13A gene. This alteration results from a C to G substitution at nucleotide position 14, causing the proline (P) at amino acid position 5 to be replaced by an arginine (R). 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