chr9-137008517-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_001606.5(ABCA2):c.7174C>T(p.Arg2392Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000628 in 1,591,676 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2392Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001606.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA2 | NM_001606.5 | c.7174C>T | p.Arg2392Trp | missense_variant | 48/49 | ENST00000341511.11 | |
ABCA2 | NM_212533.3 | c.7264C>T | p.Arg2422Trp | missense_variant | 48/49 | ||
ABCA2 | NM_001411042.1 | c.7171C>T | p.Arg2391Trp | missense_variant | 47/48 | ||
ABCA2 | XM_047422921.1 | c.7261C>T | p.Arg2421Trp | missense_variant | 47/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA2 | ENST00000341511.11 | c.7174C>T | p.Arg2392Trp | missense_variant | 48/49 | 5 | NM_001606.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000284 AC: 6AN: 211536Hom.: 0 AF XY: 0.0000174 AC XY: 2AN XY: 114872
GnomAD4 exome AF: 0.00000417 AC: 6AN: 1439352Hom.: 0 Cov.: 42 AF XY: 0.00000140 AC XY: 1AN XY: 713884
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.7264C>T (p.R2422W) alteration is located in exon 48 (coding exon 48) of the ABCA2 gene. This alteration results from a C to T substitution at nucleotide position 7264, causing the arginine (R) at amino acid position 2422 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at