2-214955289-G-A
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_173076.3(ABCA12):c.6306C>T(p.Tyr2102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 1,613,548 control chromosomes in the GnomAD database, including 135,013 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.39 ( 11635 hom., cov: 33)
Exomes 𝑓: 0.41 ( 123378 hom. )
Consequence
ABCA12
NM_173076.3 synonymous
NM_173076.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.500
Genes affected
ABCA12 (HGNC:14637): (ATP binding cassette subfamily A member 12) 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, which is the only major ABC subfamily found exclusively in multicellular eukaryotes. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 2-214955289-G-A is Benign according to our data. Variant chr2-214955289-G-A is described in ClinVar as [Benign]. Clinvar id is 262831.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-214955289-G-A is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.5 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA12 | NM_173076.3 | c.6306C>T | p.Tyr2102= | synonymous_variant | 43/53 | ENST00000272895.12 | |
SNHG31 | NR_110292.1 | n.445-6521G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA12 | ENST00000272895.12 | c.6306C>T | p.Tyr2102= | synonymous_variant | 43/53 | 1 | NM_173076.3 | P1 | |
SNHG31 | ENST00000670391.1 | n.438-6521G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.386 AC: 58710AN: 151908Hom.: 11625 Cov.: 33
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GnomAD3 exomes AF: 0.406 AC: 101921AN: 251218Hom.: 21326 AF XY: 0.412 AC XY: 55919AN XY: 135774
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GnomAD4 exome AF: 0.408 AC: 596543AN: 1461522Hom.: 123378 Cov.: 42 AF XY: 0.411 AC XY: 298803AN XY: 727096
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GnomAD4 genome AF: 0.386 AC: 58754AN: 152026Hom.: 11635 Cov.: 33 AF XY: 0.387 AC XY: 28744AN XY: 74314
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Autosomal recessive congenital ichthyosis 4A Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Congenital ichthyosis of skin Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Autosomal recessive congenital ichthyosis 4B Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at