rs28940271
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_173076.3(ABCA12):c.4615G>A(p.Glu1539Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_173076.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA12 | NM_173076.3 | c.4615G>A | p.Glu1539Lys | missense_variant | 31/53 | ENST00000272895.12 | |
ABCA12 | NM_015657.4 | c.3661G>A | p.Glu1221Lys | missense_variant | 23/45 | ||
ABCA12 | XM_011510951.3 | c.4624G>A | p.Glu1542Lys | missense_variant | 31/53 | ||
ABCA12 | NR_103740.2 | n.5113G>A | non_coding_transcript_exon_variant | 33/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA12 | ENST00000272895.12 | c.4615G>A | p.Glu1539Lys | missense_variant | 31/53 | 1 | NM_173076.3 | P1 | |
ABCA12 | ENST00000389661.4 | c.3661G>A | p.Glu1221Lys | missense_variant | 23/45 | 1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727228
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Autosomal recessive congenital ichthyosis 4A Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 15, 2003 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at