X-16834296-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_018360.3(TXLNG):c.998C>T(p.Ala333Val) variant causes a missense change. The variant allele was found at a frequency of 0.000022 in 1,092,572 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018360.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TXLNG | ENST00000380122.10 | c.998C>T | p.Ala333Val | missense_variant | Exon 7 of 10 | 1 | NM_018360.3 | ENSP00000369465.5 | ||
TXLNG | ENST00000398155.4 | c.602C>T | p.Ala201Val | missense_variant | Exon 5 of 8 | 1 | ENSP00000381222.4 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000562 AC: 1AN: 177787Hom.: 0 AF XY: 0.0000160 AC XY: 1AN XY: 62625
GnomAD4 exome AF: 0.0000220 AC: 24AN: 1092572Hom.: 0 Cov.: 28 AF XY: 0.0000167 AC XY: 6AN XY: 358412
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.998C>T (p.A333V) alteration is located in exon 7 (coding exon 7) of the TXLNG gene. This alteration results from a C to T substitution at nucleotide position 998, causing the alanine (A) at amino acid position 333 to be replaced by a valine (V). 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