NM_020129.3:c.199T>C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020129.3(LGALS14):āc.199T>Cā(p.Cys67Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 1,613,706 control chromosomes in the GnomAD database, including 365,681 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C67Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_020129.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LGALS14 | ENST00000392052.8 | c.199T>C | p.Cys67Arg | missense_variant | Exon 3 of 4 | 1 | NM_020129.3 | ENSP00000375905.2 | ||
LGALS14 | ENST00000360675.7 | c.286T>C | p.Cys96Arg | missense_variant | Exon 4 of 5 | 3 | ENSP00000353893.2 | |||
LGALS14 | ENST00000601802.1 | c.148T>C | p.Cys50Arg | missense_variant | Exon 2 of 3 | 5 | ENSP00000471660.1 |
Frequencies
GnomAD3 genomes AF: 0.681 AC: 103507AN: 151986Hom.: 36035 Cov.: 32
GnomAD3 exomes AF: 0.626 AC: 157061AN: 251074Hom.: 51812 AF XY: 0.636 AC XY: 86246AN XY: 135682
GnomAD4 exome AF: 0.667 AC: 974471AN: 1461602Hom.: 329599 Cov.: 46 AF XY: 0.668 AC XY: 486026AN XY: 727122
GnomAD4 genome AF: 0.681 AC: 103597AN: 152104Hom.: 36082 Cov.: 32 AF XY: 0.676 AC XY: 50286AN XY: 74358
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at