rs7868184
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004789.4(LHX2):c.-113G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0628 in 1,117,780 control chromosomes in the GnomAD database, including 2,565 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.077 ( 561 hom., cov: 32)
Exomes 𝑓: 0.061 ( 2004 hom. )
Consequence
LHX2
NM_004789.4 5_prime_UTR
NM_004789.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.84
Genes affected
LHX2 (HGNC:6594): (LIM homeobox 2) This gene encodes a protein belonging to a large protein family, members of which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator. The protein can recapitulate or rescue phenotypes in Drosophila caused by a related protein, suggesting conservation of function during evolution. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHX2 | NM_004789.4 | c.-113G>T | 5_prime_UTR_variant | 1/5 | ENST00000373615.9 | ||
LHX2 | XM_006717323.4 | c.-113G>T | 5_prime_UTR_variant | 1/6 | |||
LHX2 | XM_047424082.1 | c.-113G>T | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHX2 | ENST00000373615.9 | c.-113G>T | 5_prime_UTR_variant | 1/5 | 1 | NM_004789.4 | P1 | ||
LHX2 | ENST00000560961.2 | c.-3-1725G>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0768 AC: 11647AN: 151584Hom.: 562 Cov.: 32
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GnomAD4 exome AF: 0.0606 AC: 58560AN: 966086Hom.: 2004 Cov.: 13 AF XY: 0.0613 AC XY: 28489AN XY: 464514
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GnomAD4 genome ? AF: 0.0768 AC: 11656AN: 151694Hom.: 561 Cov.: 32 AF XY: 0.0760 AC XY: 5638AN XY: 74138
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ClinVar
Not reported inComputational scores
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Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at