rs547600750
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001606.5(ABCA2):āc.7175G>Cā(p.Arg2392Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000000695 in 1,438,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes š: 7.0e-7 ( 0 hom. )
Consequence
ABCA2
NM_001606.5 missense
NM_001606.5 missense
Scores
9
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.78
Genes affected
ABCA2 (HGNC:32): (ATP binding cassette subfamily A member 2) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is highly expressed in brain tissue and may play a role in macrophage lipid metabolism and neural development. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.388777).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ABCA2 | NM_001606.5 | c.7175G>C | p.Arg2392Pro | missense_variant | Exon 48 of 49 | ENST00000341511.11 | NP_001597.2 | |
| ABCA2 | NM_212533.3 | c.7265G>C | p.Arg2422Pro | missense_variant | Exon 48 of 49 | NP_997698.1 | ||
| ABCA2 | NM_001411042.1 | c.7172G>C | p.Arg2391Pro | missense_variant | Exon 47 of 48 | NP_001397971.1 | ||
| ABCA2 | XM_047422921.1 | c.7262G>C | p.Arg2421Pro | missense_variant | Exon 47 of 48 | XP_047278877.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.95e-7 AC: 1AN: 1438504Hom.: 0 Cov.: 42 AF XY: 0.00 AC XY: 0AN XY: 713428
GnomAD4 exome
AF:
AC:
1
AN:
1438504
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Cov.:
42
AF XY:
AC XY:
0
AN XY:
713428
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;.;N
REVEL
Uncertain
Sift
Uncertain
D;D;D;.;D
Sift4G
Uncertain
D;D;D;D;T
Polyphen
0.93
.;P;.;.;.
Vest4
MutPred
0.25
.;Gain of glycosylation at R2391 (P = 0.0151);.;.;.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.