9-137008515-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001606.5(ABCA2):c.7176G>A(p.Arg2392=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000209 in 1,437,490 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 (★).
Frequency
Consequence
NM_001606.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA2 | NM_001606.5 | c.7176G>A | p.Arg2392= | synonymous_variant | 48/49 | ENST00000341511.11 | |
ABCA2 | NM_212533.3 | c.7266G>A | p.Arg2422= | synonymous_variant | 48/49 | ||
ABCA2 | NM_001411042.1 | c.7173G>A | p.Arg2391= | synonymous_variant | 47/48 | ||
ABCA2 | XM_047422921.1 | c.7263G>A | p.Arg2421= | synonymous_variant | 47/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA2 | ENST00000341511.11 | c.7176G>A | p.Arg2392= | synonymous_variant | 48/49 | 5 | NM_001606.5 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1437490Hom.: 0 Cov.: 42 AF XY: 0.00 AC XY: 0AN XY: 712856
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
ABCA2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 04, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.