chr19-51380596-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001161748.2(LIM2):c.369C>T(p.Thr123=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000229 in 1,614,168 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00024 ( 2 hom. )
Consequence
LIM2
NM_001161748.2 synonymous
NM_001161748.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.49
Genes affected
LIM2 (HGNC:6610): (lens intrinsic membrane protein 2) This gene encodes an eye lens-specific protein found at the junctions of lens fiber cells, where it may contribute to cell junctional organization. It acts as a receptor for calmodulin, and may play an important role in both lens development and cataractogenesis. Mutations in this gene have been associated with cataract formation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 19-51380596-G-A is Benign according to our data. Variant chr19-51380596-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1582934.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.49 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIM2 | NM_001161748.2 | c.369C>T | p.Thr123= | synonymous_variant | 4/5 | ENST00000596399.2 | |
LIM2 | NM_030657.4 | c.495C>T | p.Thr165= | synonymous_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIM2 | ENST00000596399.2 | c.369C>T | p.Thr123= | synonymous_variant | 4/5 | 1 | NM_001161748.2 | P1 | |
LIM2 | ENST00000221973.7 | c.495C>T | p.Thr165= | synonymous_variant | 4/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152174Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251262Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135822
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GnomAD4 exome AF: 0.000244 AC: 356AN: 1461878Hom.: 2 Cov.: 38 AF XY: 0.000232 AC XY: 169AN XY: 727236
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GnomAD4 genome AF: 0.0000854 AC: 13AN: 152290Hom.: 0 Cov.: 31 AF XY: 0.0000671 AC XY: 5AN XY: 74474
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cataract 19 multiple types Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2021 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at