chr17-6996178-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000697.3(ALOX12):c.61C>A(p.Arg21Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000638 in 1,253,488 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000697.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX12 | NM_000697.3 | c.61C>A | p.Arg21Ser | missense_variant | 1/14 | ENST00000251535.11 | |
ALOX12-AS1 | NR_040089.1 | n.234-10638G>T | intron_variant, non_coding_transcript_variant | ||||
ALOX12 | XM_011523780.3 | c.61C>A | p.Arg21Ser | missense_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX12 | ENST00000251535.11 | c.61C>A | p.Arg21Ser | missense_variant | 1/14 | 1 | NM_000697.3 | P1 | |
ALOX12-AS1 | ENST00000653385.1 | n.139+16018G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.00000545 AC: 6AN: 1101268Hom.: 0 Cov.: 29 AF XY: 0.00000575 AC XY: 3AN XY: 521714
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.61C>A (p.R21S) alteration is located in exon 1 (coding exon 1) of the ALOX12 gene. This alteration results from a C to A substitution at nucleotide position 61, causing the arginine (R) at amino acid position 21 to be replaced by a serine (S). 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