rs817126
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_172232.4(ABCA5):c.3031-142T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 525,316 control chromosomes in the GnomAD database, including 32,610 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 8016 hom., cov: 31)
Exomes 𝑓: 0.35 ( 24594 hom. )
Consequence
ABCA5
NM_172232.4 intron
NM_172232.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.972
Genes affected
ABCA5 (HGNC:35): (ATP binding cassette subfamily A member 5) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This encoded protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This gene is clustered among 4 other ABC1 family members on 17q24, but neither the substrate nor the function of this gene is known. Alternative splicing of this gene results in several transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA5 | NM_172232.4 | c.3031-142T>C | intron_variant | ENST00000392676.8 | |||
ABCA5 | NM_018672.5 | c.3031-142T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA5 | ENST00000392676.8 | c.3031-142T>C | intron_variant | 1 | NM_172232.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.314 AC: 47602AN: 151808Hom.: 8013 Cov.: 31
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GnomAD4 exome AF: 0.349 AC: 130400AN: 373390Hom.: 24594 AF XY: 0.350 AC XY: 68842AN XY: 196452
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GnomAD4 genome ? AF: 0.313 AC: 47626AN: 151926Hom.: 8016 Cov.: 31 AF XY: 0.319 AC XY: 23667AN XY: 74220
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at