19-39707237-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020129.3(LGALS14):c.152C>T(p.Ala51Val) 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 1,613,996 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020129.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LGALS14 | ENST00000392052.8 | c.152C>T | p.Ala51Val | missense_variant | Exon 3 of 4 | 1 | NM_020129.3 | ENSP00000375905.2 | ||
LGALS14 | ENST00000360675.7 | c.239C>T | p.Ala80Val | missense_variant | Exon 4 of 5 | 3 | ENSP00000353893.2 | |||
LGALS14 | ENST00000601802.1 | c.101C>T | p.Ala34Val | missense_variant | Exon 2 of 3 | 5 | ENSP00000471660.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251010Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135660
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461774Hom.: 0 Cov.: 32 AF XY: 0.0000536 AC XY: 39AN XY: 727196
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.239C>T (p.A80V) alteration is located in exon 4 (coding exon 3) of the LGALS14 gene. This alteration results from a C to T substitution at nucleotide position 239, causing the alanine (A) at amino acid position 80 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