rs143473036
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001606.5(ABCA2):c.1193C>T(p.Thr398Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000326 in 1,596,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001606.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCA2 | NM_001606.5 | c.1193C>T | p.Thr398Met | missense_variant | Exon 9 of 49 | ENST00000341511.11 | NP_001597.2 | |
ABCA2 | NM_212533.3 | c.1283C>T | p.Thr428Met | missense_variant | Exon 9 of 49 | NP_997698.1 | ||
ABCA2 | NM_001411042.1 | c.1190C>T | p.Thr397Met | missense_variant | Exon 8 of 48 | NP_001397971.1 | ||
ABCA2 | XM_047422921.1 | c.1280C>T | p.Thr427Met | missense_variant | Exon 8 of 48 | XP_047278877.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000499 AC: 11AN: 220462Hom.: 0 AF XY: 0.0000327 AC XY: 4AN XY: 122344
GnomAD4 exome AF: 0.0000277 AC: 40AN: 1444306Hom.: 0 Cov.: 31 AF XY: 0.0000251 AC XY: 18AN XY: 717860
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74504
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at