rs11890468
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_173076.3(ABCA12):āc.821A>Gā(p.Gln274Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00657 in 1,613,578 control chromosomes in the GnomAD database, including 570 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_173076.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA12 | NM_173076.3 | c.821A>G | p.Gln274Arg | missense_variant | 7/53 | ENST00000272895.12 | |
ABCA12 | XM_011510951.3 | c.821A>G | p.Gln274Arg | missense_variant | 7/53 | ||
ABCA12 | NR_103740.2 | n.1263A>G | non_coding_transcript_exon_variant | 8/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA12 | ENST00000272895.12 | c.821A>G | p.Gln274Arg | missense_variant | 7/53 | 1 | NM_173076.3 | P1 | |
ENST00000628464.2 | n.1021+1371T>C | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000626134.2 | n.404+1371T>C | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000626771.1 | n.338+1371T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0349 AC: 5313AN: 152166Hom.: 292 Cov.: 32
GnomAD3 exomes AF: 0.00923 AC: 2312AN: 250430Hom.: 128 AF XY: 0.00672 AC XY: 910AN XY: 135364
GnomAD4 exome AF: 0.00361 AC: 5269AN: 1461294Hom.: 276 Cov.: 31 AF XY: 0.00304 AC XY: 2213AN XY: 726960
GnomAD4 genome ? AF: 0.0350 AC: 5327AN: 152284Hom.: 294 Cov.: 32 AF XY: 0.0334 AC XY: 2489AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Dec 22, 2015 | - - |
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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at