chr16-2298656-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001089.3(ABCA3):c.1742-116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 1,308,700 control chromosomes in the GnomAD database, including 115,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.43 ( 14147 hom., cov: 29)
Exomes 𝑓: 0.42 ( 101040 hom. )
Consequence
ABCA3
NM_001089.3 intron
NM_001089.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.03
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=-1.02).
BP6
Variant 16-2298656-A-G is Benign according to our data. Variant chr16-2298656-A-G is described in ClinVar as [Benign]. Clinvar id is 1287357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCA3 | NM_001089.3 | c.1742-116T>C | intron_variant | ENST00000301732.10 | NP_001080.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCA3 | ENST00000301732.10 | c.1742-116T>C | intron_variant | 1 | NM_001089.3 | ENSP00000301732.5 | ||||
ABCA3 | ENST00000382381.7 | c.1568-116T>C | intron_variant | 1 | ENSP00000371818.3 | |||||
ABCA3 | ENST00000563623.5 | n.2305-116T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.430 AC: 65043AN: 151132Hom.: 14140 Cov.: 29
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GnomAD4 exome AF: 0.416 AC: 481663AN: 1157452Hom.: 101040 AF XY: 0.420 AC XY: 243519AN XY: 580050
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GnomAD4 genome AF: 0.430 AC: 65079AN: 151248Hom.: 14147 Cov.: 29 AF XY: 0.430 AC XY: 31745AN XY: 73840
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at