chr10-97584744-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_138413.4(HOGA1):c.41T>A(p.Leu14Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,658 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L14L) has been classified as Likely benign.
Frequency
Consequence
NM_138413.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOGA1 | NM_138413.4 | c.41T>A | p.Leu14Gln | missense_variant | 1/7 | ENST00000370646.9 | |
HOGA1 | NM_001134670.2 | c.41T>A | p.Leu14Gln | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOGA1 | ENST00000370646.9 | c.41T>A | p.Leu14Gln | missense_variant | 1/7 | 1 | NM_138413.4 | P1 | |
HOGA1 | ENST00000370647.8 | c.41T>A | p.Leu14Gln | missense_variant | 1/3 | 1 | |||
HOGA1 | ENST00000465608.1 | n.422T>A | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250154Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135092
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460452Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726328
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
Primary hyperoxaluria type 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | curation | Clinical Biochemistry Laboratory, Health Services Laboratory | Oct 27, 2023 | ACMG:PM1 PM3 PP3 BP1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at