chr22-37678538-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_002305.4(LGALS1):c.145C>T(p.Arg49Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,613,652 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002305.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LGALS1 | NM_002305.4 | c.145C>T | p.Arg49Cys | missense_variant | Exon 3 of 4 | ENST00000215909.10 | NP_002296.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250478Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135782
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461278Hom.: 1 Cov.: 35 AF XY: 0.0000138 AC XY: 10AN XY: 726934
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152374Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.145C>T (p.R49C) alteration is located in exon 3 (coding exon 3) of the LGALS1 gene. This alteration results from a C to T substitution at nucleotide position 145, causing the arginine (R) at amino acid position 49 to be replaced by a cysteine (C). 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