chr7-48219460-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152701.5(ABCA13):c.394G>A(p.Ala132Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000182 in 1,612,874 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 1 hom. )
Consequence
ABCA13
NM_152701.5 missense
NM_152701.5 missense
Scores
2
4
11
Clinical Significance
Conservation
PhyloP100: 4.74
Genes affected
ABCA13 (HGNC:14638): (ATP binding cassette subfamily A member 13) In human, the ATP-binding cassette (ABC) family of transmembrane transporters has at least 48 genes and 7 gene subfamilies. This gene is a member of ABC gene subfamily A (ABCA). Genes within the ABCA family typically encode several thousand amino acids. Like other ABC transmembrane transporter proteins, this protein has 12 or more transmembrane alpha-helix domains that likely arrange to form a single central chamber with multiple substrate binding sites. It is also predicted to have two large extracellular domains and two nucleotide binding domains as is typical for ABCA proteins. Alternative splice variants have been described but their biological validity has not been demonstrated.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.098281235).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA13 | NM_152701.5 | c.394G>A | p.Ala132Thr | missense_variant | 4/62 | ENST00000435803.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA13 | ENST00000435803.6 | c.394G>A | p.Ala132Thr | missense_variant | 4/62 | 1 | NM_152701.5 | P1 | |
ABCA13 | ENST00000417403.5 | c.394G>A | p.Ala132Thr | missense_variant, NMD_transcript_variant | 4/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152110Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000238 AC: 59AN: 248018Hom.: 0 AF XY: 0.000268 AC XY: 36AN XY: 134544
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GnomAD4 exome AF: 0.000188 AC: 275AN: 1460646Hom.: 1 Cov.: 30 AF XY: 0.000208 AC XY: 151AN XY: 726582
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GnomAD4 genome AF: 0.000125 AC: 19AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74424
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.394G>A (p.A132T) alteration is located in exon 4 (coding exon 4) of the ABCA13 gene. This alteration results from a G to A substitution at nucleotide position 394, causing the alanine (A) at amino acid position 132 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Pathogenic
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
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