chr2-214989432-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_173076.3(ABCA12):c.3726G>A(p.Pro1242=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0607 in 1,612,962 control chromosomes in the GnomAD database, including 3,887 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1242P) has been classified as Likely benign.
Frequency
Consequence
NM_173076.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA12 | NM_173076.3 | c.3726G>A | p.Pro1242= | synonymous_variant | 26/53 | ENST00000272895.12 | |
ABCA12 | NM_015657.4 | c.2772G>A | p.Pro924= | synonymous_variant | 18/45 | ||
ABCA12 | XM_011510951.3 | c.3726G>A | p.Pro1242= | synonymous_variant | 26/53 | ||
ABCA12 | NR_103740.2 | n.4224G>A | non_coding_transcript_exon_variant | 28/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA12 | ENST00000272895.12 | c.3726G>A | p.Pro1242= | synonymous_variant | 26/53 | 1 | NM_173076.3 | P1 | |
ABCA12 | ENST00000389661.4 | c.2772G>A | p.Pro924= | synonymous_variant | 18/45 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0740 AC: 11178AN: 151076Hom.: 544 Cov.: 30
GnomAD3 exomes AF: 0.0723 AC: 18183AN: 251464Hom.: 1099 AF XY: 0.0672 AC XY: 9133AN XY: 135906
GnomAD4 exome AF: 0.0593 AC: 86689AN: 1461772Hom.: 3337 Cov.: 31 AF XY: 0.0586 AC XY: 42618AN XY: 727198
GnomAD4 genome AF: 0.0741 AC: 11200AN: 151190Hom.: 550 Cov.: 30 AF XY: 0.0739 AC XY: 5453AN XY: 73796
ClinVar
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at