rs62453384
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The ENST00000404938.7(ABCB5):c.2429G>A(p.Gly810Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000892 in 1,613,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000094 ( 0 hom. )
Consequence
ABCB5
ENST00000404938.7 missense
ENST00000404938.7 missense
Scores
5
9
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.44
Genes affected
ABCB5 (HGNC:46): (ATP binding cassette subfamily B member 5) ABCB5 belongs to the ATP-binding cassette (ABC) transporter superfamily of integral membrane proteins. These proteins participate in ATP-dependent transmembrane transport of structurally diverse molecules ranging from small ions, sugars, and peptides to more complex organic molecules (Chen et al., 2005 [PubMed 15760339]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.922
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCB5 | NM_001163941.2 | c.2429G>A | p.Gly810Asp | missense_variant | 21/28 | ENST00000404938.7 | NP_001157413.1 | |
ABCB5 | NM_178559.6 | c.1094G>A | p.Gly365Asp | missense_variant | 12/19 | NP_848654.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCB5 | ENST00000404938.7 | c.2429G>A | p.Gly810Asp | missense_variant | 21/28 | 1 | NM_001163941.2 | ENSP00000384881 | P1 | |
ABCB5 | ENST00000258738.10 | c.1094G>A | p.Gly365Asp | missense_variant | 12/19 | 1 | ENSP00000258738 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151930Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000123 AC: 31AN: 251022Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135712
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GnomAD4 exome AF: 0.0000937 AC: 137AN: 1461714Hom.: 0 Cov.: 35 AF XY: 0.0000963 AC XY: 70AN XY: 727178
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152048Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74332
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
.;M
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Pathogenic
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Vest4
MutPred
0.91
.;Loss of methylation at R367 (P = 0.0693);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at