chr17-68990852-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_080283.4(ABCA9):c.3822G>A(p.Val1274=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
ABCA9
NM_080283.4 synonymous
NM_080283.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.345
Genes affected
ABCA9 (HGNC:39): (ATP binding cassette subfamily A member 9) This gene is a member of the superfamily of ATP-binding cassette (ABC) transporters and the encoded protein contains two transmembrane domains and two nucleotide binding folds. 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 gene is a member of the ABC1 subfamily and is clustered with four other ABC1 family members on chromosome 17q24. Transcriptional expression of this gene is induced during monocyte differentiation into macrophages and is suppressed by cholesterol import. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 17-68990852-C-T is Benign according to our data. Variant chr17-68990852-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648157.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.345 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA9 | NM_080283.4 | c.3822G>A | p.Val1274= | synonymous_variant | 29/39 | ENST00000340001.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA9 | ENST00000340001.9 | c.3822G>A | p.Val1274= | synonymous_variant | 29/39 | 1 | NM_080283.4 | P1 | |
ABCA9-AS1 | ENST00000630625.1 | n.378-21131C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
ABCA9 | ENST00000453985.6 | c.3708G>A | p.Val1236= | synonymous_variant | 28/38 | 5 | |||
ABCA9 | ENST00000460872.1 | n.614G>A | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152190Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250348Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135316
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GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460870Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726746
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74350
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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 | Apr 01, 2023 | ABCA9: BP4, BP7 - |
Computational scores
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Benign
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Benign
DANN
Benign
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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