rs2066882
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005502.4(ABCA1):c.6401+117A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 866,942 control chromosomes in the GnomAD database, including 7,061 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.11 ( 1216 hom., cov: 34)
Exomes 𝑓: 0.10 ( 5845 hom. )
Consequence
ABCA1
NM_005502.4 intron
NM_005502.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.916
Genes affected
ABCA1 (HGNC:29): (ATP binding cassette subfamily A member 1) 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. With cholesterol as its substrate, this protein functions as a cholesteral efflux pump in the cellular lipid removal pathway. Mutations in both alleles of this gene cause Tangier disease and familial high-density lipoprotein (HDL) deficiency. [provided by RefSeq, Sep 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 9-104786181-T-C is Benign according to our data. Variant chr9-104786181-T-C is described in ClinVar as [Benign]. Clinvar id is 1287036.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-104786181-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA1 | NM_005502.4 | c.6401+117A>G | intron_variant | ENST00000374736.8 | |||
NIPSNAP3B | XR_007061325.1 | n.960-1436T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA1 | ENST00000374736.8 | c.6401+117A>G | intron_variant | 1 | NM_005502.4 | P1 | |||
ABCA1 | ENST00000678995.1 | c.6407+117A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.106 AC: 16121AN: 152182Hom.: 1210 Cov.: 34
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GnomAD4 exome AF: 0.102 AC: 73093AN: 714642Hom.: 5845 AF XY: 0.106 AC XY: 40372AN XY: 379646
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GnomAD4 genome ? AF: 0.106 AC: 16148AN: 152300Hom.: 1216 Cov.: 34 AF XY: 0.107 AC XY: 7935AN XY: 74460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 07, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at