rs141621969
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001089.3(ABCA3):c.1502C>T(p.Ala501Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,613,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A501E) has been classified as Likely benign.
Frequency
Consequence
NM_001089.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA3 | NM_001089.3 | c.1502C>T | p.Ala501Val | missense_variant | 13/33 | ENST00000301732.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA3 | ENST00000301732.10 | c.1502C>T | p.Ala501Val | missense_variant | 13/33 | 1 | NM_001089.3 | P1 | |
ABCA3 | ENST00000382381.7 | c.1328C>T | p.Ala443Val | missense_variant | 12/32 | 1 | |||
ABCA3 | ENST00000563623.5 | n.2065C>T | non_coding_transcript_exon_variant | 13/20 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000726 AC: 11AN: 151566Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251412Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135876
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461794Hom.: 0 Cov.: 32 AF XY: 0.0000756 AC XY: 55AN XY: 727194
GnomAD4 genome ? AF: 0.0000726 AC: 11AN: 151566Hom.: 0 Cov.: 30 AF XY: 0.0000541 AC XY: 4AN XY: 73986
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at