17-69086646-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_080284.3(ABCA6):āc.3909A>Gā(p.Ala1303=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00647 in 1,612,284 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0054 ( 3 hom., cov: 30)
Exomes š: 0.0066 ( 67 hom. )
Consequence
ABCA6
NM_080284.3 synonymous
NM_080284.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.14
Genes affected
ABCA6 (HGNC:36): (ATP binding cassette subfamily A member 6) 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, and White). This encoded 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 gene is clustered among 4 other ABC1 family members on 17q24 and may play a role in macrophage lipid homeostasis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 17-69086646-T-C is Benign according to our data. Variant chr17-69086646-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2648162.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.14 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCA6 | NM_080284.3 | c.3909A>G | p.Ala1303= | synonymous_variant | 30/39 | ENST00000284425.7 | NP_525023.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCA6 | ENST00000284425.7 | c.3909A>G | p.Ala1303= | synonymous_variant | 30/39 | 1 | NM_080284.3 | ENSP00000284425 | P1 | |
ABCA6 | ENST00000446604.6 | n.1175A>G | non_coding_transcript_exon_variant | 9/18 | 2 | |||||
ABCA6 | ENST00000589482.1 | n.356A>G | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00538 AC: 819AN: 152102Hom.: 3 Cov.: 30
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GnomAD3 exomes AF: 0.00608 AC: 1528AN: 251164Hom.: 11 AF XY: 0.00662 AC XY: 899AN XY: 135784
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GnomAD4 exome AF: 0.00658 AC: 9613AN: 1460064Hom.: 67 Cov.: 29 AF XY: 0.00684 AC XY: 4970AN XY: 726488
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GnomAD4 genome AF: 0.00538 AC: 819AN: 152220Hom.: 3 Cov.: 30 AF XY: 0.00619 AC XY: 461AN XY: 74434
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | ABCA6: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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