rs28937314
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_005502.4(ABCA1):c.2803A>G(p.Asn935Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,628 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N935H) has been classified as Pathogenic.
Frequency
Consequence
NM_005502.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA1 | NM_005502.4 | c.2803A>G | p.Asn935Asp | missense_variant | 19/50 | ENST00000374736.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA1 | ENST00000374736.8 | c.2803A>G | p.Asn935Asp | missense_variant | 19/50 | 1 | NM_005502.4 | P1 | |
ABCA1 | ENST00000678995.1 | c.2803A>G | p.Asn935Asp | missense_variant | 19/50 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461628Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727120
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Tangier disease Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Baylor Genetics | May 01, 2016 | Our laboratory reported two molecular diagnoses in CPOX (NM_000097.5:c.1339C>T) and ABCA1 (NM_005502.3:c.2803A>G) in an individual with splenomegaly, hemosiderosis, recurrent skin ulcerations, recent cognitive decline, headaches, abdominal pain, extremely low levels of cholesterol, and upper extremity paresthesias. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at