rs11817730
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_138413.4(HOGA1):c.212-21A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 1,613,546 control chromosomes in the GnomAD database, including 31,362 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_138413.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOGA1 | NM_138413.4 | c.212-21A>G | intron_variant | ENST00000370646.9 | |||
HOGA1 | NM_001134670.2 | c.212-3103A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOGA1 | ENST00000370646.9 | c.212-21A>G | intron_variant | 1 | NM_138413.4 | P1 | |||
HOGA1 | ENST00000370647.8 | c.212-3103A>G | intron_variant | 1 | |||||
HOGA1 | ENST00000465608.1 | n.593-21A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.196 AC: 29882AN: 152074Hom.: 3045 Cov.: 32
GnomAD3 exomes AF: 0.185 AC: 46483AN: 251460Hom.: 4437 AF XY: 0.184 AC XY: 25015AN XY: 135906
GnomAD4 exome AF: 0.195 AC: 284464AN: 1461354Hom.: 28312 Cov.: 34 AF XY: 0.194 AC XY: 141039AN XY: 726992
GnomAD4 genome ? AF: 0.197 AC: 29917AN: 152192Hom.: 3050 Cov.: 32 AF XY: 0.195 AC XY: 14542AN XY: 74406
ClinVar
Submissions by phenotype
Primary hyperoxaluria type 3 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Uncertain significance, no assertion criteria provided | research | Clinical Biochemistry Laboratory, Health Services Laboratory | Nov 27, 2014 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at