chr14-55142700-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002306.4(LGALS3):c.548G>A(p.Arg183Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00489 in 1,613,880 control chromosomes in the GnomAD database, including 326 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002306.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGALS3 | NM_002306.4 | c.548G>A | p.Arg183Lys | missense_variant | 5/6 | ENST00000254301.14 | |
LGALS3 | NM_001357678.2 | c.590G>A | p.Arg197Lys | missense_variant | 6/7 | ||
LGALS3 | NR_003225.2 | n.1592G>A | non_coding_transcript_exon_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGALS3 | ENST00000254301.14 | c.548G>A | p.Arg183Lys | missense_variant | 5/6 | 1 | NM_002306.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0258 AC: 3920AN: 152166Hom.: 164 Cov.: 32
GnomAD3 exomes AF: 0.00689 AC: 1719AN: 249528Hom.: 77 AF XY: 0.00553 AC XY: 748AN XY: 135384
GnomAD4 exome AF: 0.00272 AC: 3973AN: 1461596Hom.: 162 Cov.: 30 AF XY: 0.00239 AC XY: 1738AN XY: 727128
GnomAD4 genome AF: 0.0258 AC: 3926AN: 152284Hom.: 164 Cov.: 32 AF XY: 0.0247 AC XY: 1840AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at