chr9-137008616-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_001606.5(ABCA2):c.7075G>A(p.Val2359Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000687 in 1,455,770 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V2359L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001606.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA2 | NM_001606.5 | c.7075G>A | p.Val2359Met | missense_variant | 48/49 | ENST00000341511.11 | |
ABCA2 | NM_212533.3 | c.7165G>A | p.Val2389Met | missense_variant | 48/49 | ||
ABCA2 | NM_001411042.1 | c.7072G>A | p.Val2358Met | missense_variant | 47/48 | ||
ABCA2 | XM_047422921.1 | c.7162G>A | p.Val2388Met | missense_variant | 47/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA2 | ENST00000341511.11 | c.7075G>A | p.Val2359Met | missense_variant | 48/49 | 5 | NM_001606.5 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000423 AC: 1AN: 236616Hom.: 0 AF XY: 0.00000777 AC XY: 1AN XY: 128638
GnomAD4 exome AF: 0.00000687 AC: 10AN: 1455770Hom.: 0 Cov.: 42 AF XY: 0.00000691 AC XY: 5AN XY: 723522
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.7165G>A (p.V2389M) alteration is located in exon 48 (coding exon 48) of the ABCA2 gene. This alteration results from a G to A substitution at nucleotide position 7165, causing the valine (V) at amino acid position 2389 to be replaced by a methionine (M). 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