chr11-63515597-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033101.4(LGALS12):c.682G>A(p.Ala228Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000991 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A228V) has been classified as Likely benign.
Frequency
Consequence
NM_033101.4 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 | UniProt |
---|---|---|---|---|---|---|---|
LGALS12 | NM_033101.4 | c.682G>A | p.Ala228Thr | missense_variant | 8/9 | ENST00000394618.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGALS12 | ENST00000394618.9 | c.682G>A | p.Ala228Thr | missense_variant | 8/9 | 1 | NM_033101.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000499 AC: 76AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251268Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135822
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.0000481 AC XY: 35AN XY: 727236
GnomAD4 genome ? AF: 0.000499 AC: 76AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000538 AC XY: 40AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.751G>A (p.A251T) alteration is located in exon 8 (coding exon 8) of the LGALS12 gene. This alteration results from a G to A substitution at nucleotide position 751, causing the alanine (A) at amino acid position 251 to be replaced by a threonine (T). 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