rs773223403
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PM2PP3_StrongPP5_Moderate
The NM_001089.3(ABCA3):c.614-2A>G variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_001089.3 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA3 | NM_001089.3 | c.614-2A>G | splice_acceptor_variant | ENST00000301732.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA3 | ENST00000301732.10 | c.614-2A>G | splice_acceptor_variant | 1 | NM_001089.3 | P1 | |||
ABCA3 | ENST00000382381.7 | c.614-2A>G | splice_acceptor_variant | 1 | |||||
ABCA3 | ENST00000563623.5 | n.1177-2A>G | splice_acceptor_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249002Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134856
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461354Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 726964
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Respiratory distress;C2973725:Pulmonary arterial hypertension;C4281993:Neonatal respiratory distress Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Center for Personalized Medicine, Children's Hospital Los Angeles | - | - - |
See cases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Center for Personalized Medicine, Children's Hospital Los Angeles | Dec 21, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at