15-48756263-C-T
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001194998.2(CEP152):c.2985G>A(p.Ala995Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000754 in 1,590,852 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 (★). Synonymous variant affecting the same amino acid position (i.e. A995A) has been classified as Likely benign.
Frequency
Consequence
NM_001194998.2 synonymous
Scores
Clinical Significance
Conservation
Publications
- microcephaly with or without short statureInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- Seckel syndrome 5Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
- microcephaly 9, primary, autosomal recessiveInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- autosomal recessive primary microcephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Seckel syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950.7 | c.2985G>A | p.Ala995Ala | synonymous_variant | Exon 20 of 27 | 1 | NM_001194998.2 | ENSP00000370337.2 | ||
CEP152 | ENST00000399334.7 | c.2985G>A | p.Ala995Ala | synonymous_variant | Exon 20 of 26 | 1 | ENSP00000382271.3 | |||
CEP152 | ENST00000325747.9 | c.2706G>A | p.Ala902Ala | synonymous_variant | Exon 19 of 25 | 1 | ENSP00000321000.5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152082Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000213 AC: 5AN: 234956 AF XY: 0.0000157 show subpopulations
GnomAD4 exome AF: 0.00000695 AC: 10AN: 1438770Hom.: 0 Cov.: 32 AF XY: 0.00000842 AC XY: 6AN XY: 712966 show subpopulations
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74272 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at