4-41494537-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000313860.12(LIMCH1):āc.98A>Gā(p.Gln33Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000137 in 1,458,048 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000313860.12 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIMCH1 | NM_001330787.2 | c.98A>G | p.Gln33Arg | missense_variant, splice_region_variant | 2/27 | ||
LIMCH1 | NM_014988.5 | c.98A>G | p.Gln33Arg | missense_variant, splice_region_variant | 2/27 | ||
LIMCH1 | NM_001330790.2 | c.98A>G | p.Gln33Arg | missense_variant, splice_region_variant | 2/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIMCH1 | ENST00000313860.12 | c.98A>G | p.Gln33Arg | missense_variant, splice_region_variant | 2/27 | 1 | P3 | ||
LIMCH1 | ENST00000512820.5 | c.98A>G | p.Gln33Arg | missense_variant, splice_region_variant | 2/26 | 1 | |||
LIMCH1 | ENST00000512946.5 | c.98A>G | p.Gln33Arg | missense_variant, splice_region_variant | 2/26 | 1 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247750Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133662
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458048Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 725020
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at