19-18884248-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The ENST00000623882.4(CERS1):āc.429A>Gā(p.Ala143=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,612,910 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. A143A) has been classified as Likely benign.
Frequency
Consequence
ENST00000623882.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CERS1 | NM_021267.5 | c.429A>G | p.Ala143= | synonymous_variant | 3/8 | ENST00000623882.4 | NP_067090.1 | |
GDF1 | NM_001492.6 | c.-894A>G | 5_prime_UTR_variant | 3/8 | ENST00000247005.8 | NP_001483.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CERS1 | ENST00000623882.4 | c.429A>G | p.Ala143= | synonymous_variant | 3/8 | 1 | NM_021267.5 | ENSP00000485308 | P2 | |
GDF1 | ENST00000247005.8 | c.-894A>G | 5_prime_UTR_variant | 3/8 | 1 | NM_001492.6 | ENSP00000247005 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000849 AC: 129AN: 152020Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000254 AC: 62AN: 244084Hom.: 0 AF XY: 0.000233 AC XY: 31AN XY: 132974
GnomAD4 exome AF: 0.000136 AC: 198AN: 1460772Hom.: 1 Cov.: 31 AF XY: 0.000131 AC XY: 95AN XY: 726618
GnomAD4 genome AF: 0.000848 AC: 129AN: 152138Hom.: 0 Cov.: 31 AF XY: 0.000807 AC XY: 60AN XY: 74370
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 15, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Progressive myoclonic epilepsy type 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at