chr9-136197833-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_178138.6(LHX3):c.776-90C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 1,422,906 control chromosomes in the GnomAD database, including 216,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.55 ( 23154 hom., cov: 33)
Exomes 𝑓: 0.55 ( 193493 hom. )
Consequence
LHX3
NM_178138.6 intron
NM_178138.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.721
Genes affected
LHX3 (HGNC:6595): (LIM homeobox 3) This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 9-136197833-G-A is Benign according to our data. Variant chr9-136197833-G-A is described in ClinVar as [Benign]. Clinvar id is 1185281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHX3 | NM_178138.6 | c.776-90C>T | intron_variant | ENST00000371748.10 | |||
LHX3 | NM_001363746.1 | c.743-90C>T | intron_variant | ||||
LHX3 | NM_014564.5 | c.791-90C>T | intron_variant | ||||
LHX3 | XM_017015168.1 | c.704-90C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHX3 | ENST00000371748.10 | c.776-90C>T | intron_variant | 1 | NM_178138.6 | ||||
LHX3 | ENST00000371746.9 | c.791-90C>T | intron_variant | 1 | P1 | ||||
LHX3 | ENST00000619587.1 | c.743-90C>T | intron_variant | 1 | |||||
LHX3 | ENST00000645419.1 | n.1601-90C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.548 AC: 83266AN: 151960Hom.: 23135 Cov.: 33
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GnomAD4 exome AF: 0.549 AC: 697469AN: 1270828Hom.: 193493 AF XY: 0.546 AC XY: 347628AN XY: 636214
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GnomAD4 genome AF: 0.548 AC: 83320AN: 152078Hom.: 23154 Cov.: 33 AF XY: 0.543 AC XY: 40352AN XY: 74332
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Non-acquired combined pituitary hormone deficiency with spine abnormalities Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at