17-6998570-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000697.3(ALOX12):c.399A>C(p.Lys133Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000806 in 1,613,986 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000697.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALOX12 | NM_000697.3 | c.399A>C | p.Lys133Asn | missense_variant | Exon 3 of 14 | ENST00000251535.11 | NP_000688.2 | |
ALOX12 | XM_011523780.3 | c.399A>C | p.Lys133Asn | missense_variant | Exon 3 of 13 | XP_011522082.2 | ||
ALOX12-AS1 | NR_040089.1 | n.233+11226T>G | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000821 AC: 125AN: 152182Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00140 AC: 352AN: 251072Hom.: 2 AF XY: 0.00144 AC XY: 195AN XY: 135844
GnomAD4 exome AF: 0.000804 AC: 1175AN: 1461686Hom.: 7 Cov.: 31 AF XY: 0.000829 AC XY: 603AN XY: 727158
GnomAD4 genome AF: 0.000827 AC: 126AN: 152300Hom.: 0 Cov.: 31 AF XY: 0.000739 AC XY: 55AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
ALOX12: BP4, BS1 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at