chr13-30735647-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_001629.4(ALOX5AP):c.42C>T(p.Ile14Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000942 in 1,614,124 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001629.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALOX5AP | NM_001629.4 | c.42C>T | p.Ile14Ile | synonymous_variant | Exon 1 of 5 | ENST00000380490.5 | NP_001620.2 | |
ALOX5AP | NM_001204406.2 | c.213C>T | p.Ile71Ile | synonymous_variant | Exon 2 of 6 | NP_001191335.1 | ||
LOC124903146 | XR_007063743.1 | n.221-2910G>A | intron_variant | Intron 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALOX5AP | ENST00000380490.5 | c.42C>T | p.Ile14Ile | synonymous_variant | Exon 1 of 5 | 1 | NM_001629.4 | ENSP00000369858.3 | ||
ALOX5AP | ENST00000617770.4 | c.213C>T | p.Ile71Ile | synonymous_variant | Exon 2 of 6 | 1 | ENSP00000479870.1 |
Frequencies
GnomAD3 genomes AF: 0.00450 AC: 685AN: 152120Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00122 AC: 306AN: 251436Hom.: 4 AF XY: 0.000920 AC XY: 125AN XY: 135898
GnomAD4 exome AF: 0.000567 AC: 829AN: 1461886Hom.: 9 Cov.: 35 AF XY: 0.000528 AC XY: 384AN XY: 727240
GnomAD4 genome AF: 0.00455 AC: 692AN: 152238Hom.: 8 Cov.: 32 AF XY: 0.00443 AC XY: 330AN XY: 74436
ClinVar
Submissions by phenotype
ALOX5AP-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at