rs2230805
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_005502.4(ABCA1):āc.474G>Cā(p.Leu158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L158L) has been classified as Benign.
Frequency
Consequence
NM_005502.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA1 | NM_005502.4 | c.474G>C | p.Leu158= | synonymous_variant | 6/50 | ENST00000374736.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA1 | ENST00000374736.8 | c.474G>C | p.Leu158= | synonymous_variant | 6/50 | 1 | NM_005502.4 | P1 | |
ABCA1 | ENST00000678995.1 | c.474G>C | p.Leu158= | synonymous_variant | 6/50 | ||||
ABCA1 | ENST00000423487.6 | c.474G>C | p.Leu158= | synonymous_variant | 6/8 | 2 | |||
ABCA1 | ENST00000374733.1 | c.294G>C | p.Leu98= | synonymous_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151378Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251444Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135892
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461658Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 727134
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151496Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 73962
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2019 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at