rs323043
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001089.3(ABCA3):c.1755C>T(p.Pro585=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P585P) has been classified as Benign.
Frequency
Consequence
NM_001089.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA3 | NM_001089.3 | c.1755C>T | p.Pro585= | synonymous_variant | 15/33 | ENST00000301732.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA3 | ENST00000301732.10 | c.1755C>T | p.Pro585= | synonymous_variant | 15/33 | 1 | NM_001089.3 | P1 | |
ABCA3 | ENST00000382381.7 | c.1581C>T | p.Pro527= | synonymous_variant | 14/32 | 1 | |||
ABCA3 | ENST00000563623.5 | n.2318C>T | non_coding_transcript_exon_variant | 15/20 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251100Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135776
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461296Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 726958
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74306
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at