rs13332547
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001089.3(ABCA3):c.991-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 1,612,662 control chromosomes in the GnomAD database, including 16,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.13 ( 1712 hom., cov: 31)
Exomes 𝑓: 0.12 ( 14954 hom. )
Consequence
ABCA3
NM_001089.3 intron
NM_001089.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.113
Genes affected
ABCA3 (HGNC:33): (ATP binding cassette subfamily A member 3) 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, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. The full transporter encoded by this gene may be involved in development of resistance to xenobiotics and engulfment during programmed cell death. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 16-2317423-G-A is Benign according to our data. Variant chr16-2317423-G-A is described in ClinVar as [Benign]. Clinvar id is 1249107.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA3 | NM_001089.3 | c.991-20C>T | intron_variant | ENST00000301732.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA3 | ENST00000301732.10 | c.991-20C>T | intron_variant | 1 | NM_001089.3 | P1 | |||
ABCA3 | ENST00000382381.7 | c.991-20C>T | intron_variant | 1 | |||||
ABCA3 | ENST00000563623.5 | n.1554-20C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.127 AC: 19345AN: 151948Hom.: 1699 Cov.: 31
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GnomAD3 exomes AF: 0.172 AC: 43008AN: 249976Hom.: 5790 AF XY: 0.162 AC XY: 21960AN XY: 135270
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GnomAD4 exome AF: 0.121 AC: 177303AN: 1460596Hom.: 14954 Cov.: 33 AF XY: 0.121 AC XY: 88071AN XY: 726570
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GnomAD4 genome ? AF: 0.128 AC: 19400AN: 152066Hom.: 1712 Cov.: 31 AF XY: 0.134 AC XY: 9982AN XY: 74336
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 21, 2018 | - - |
Hereditary pulmonary alveolar proteinosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2015 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
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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