19-51380233-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001161748.2(LIM2):c.490C>T(p.His164Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,613,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001161748.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIM2 | ENST00000596399.2 | c.490C>T | p.His164Tyr | missense_variant | Exon 5 of 5 | 1 | NM_001161748.2 | ENSP00000472090.2 | ||
LIM2 | ENST00000221973.7 | c.616C>T | p.His206Tyr | missense_variant | Exon 5 of 5 | 1 | ENSP00000221973.2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152038Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 247972Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134270
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461604Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727056
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74388
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.616C>T (p.H206Y) alteration is located in exon 5 (coding exon 4) of the LIM2 gene. This alteration results from a C to T substitution at nucleotide position 616, causing the histidine (H) at amino acid position 206 to be replaced by a tyrosine (Y). 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