chr10-124461974-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022126.4(LHPP):āc.112G>Cā(p.Glu38Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000156 in 1,219,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E38G) has been classified as Uncertain significance.
Frequency
Consequence
NM_022126.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHPP | NM_022126.4 | c.112G>C | p.Glu38Gln | missense_variant | 1/7 | ENST00000368842.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHPP | ENST00000368842.10 | c.112G>C | p.Glu38Gln | missense_variant | 1/7 | 1 | NM_022126.4 | P1 | |
LHPP | ENST00000368839.1 | c.112G>C | p.Glu38Gln | missense_variant | 1/6 | 1 | |||
LHPP | ENST00000392757.8 | c.112G>C | p.Glu38Gln | missense_variant | 1/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 151906Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000468 AC: 5AN: 1067934Hom.: 0 Cov.: 33 AF XY: 0.00000396 AC XY: 2AN XY: 504520
GnomAD4 genome AF: 0.0000921 AC: 14AN: 152014Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 07, 2024 | The c.112G>C (p.E38Q) alteration is located in exon 1 (coding exon 1) of the LHPP gene. This alteration results from a G to C substitution at nucleotide position 112, causing the glutamic acid (E) at amino acid position 38 to be replaced by a glutamine (Q). 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