4-55974750-A-G
Variant summary
Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_025009.5(CEP135):c.1254A>G(p.Arg418Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000468 in 1,610,356 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 Likely benign (★★).
Frequency
Consequence
NM_025009.5 synonymous
Scores
Clinical Significance
Conservation
Publications
- microcephaly 8, primary, autosomal recessiveInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- autosomal recessive primary microcephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP135 | NM_025009.5 | c.1254A>G | p.Arg418Arg | synonymous_variant | Exon 11 of 26 | ENST00000257287.5 | NP_079285.2 | |
CEP135 | XM_006714055.4 | c.1221A>G | p.Arg407Arg | synonymous_variant | Exon 11 of 26 | XP_006714118.1 | ||
CEP135 | XM_005265788.5 | c.183A>G | p.Arg61Arg | synonymous_variant | Exon 4 of 19 | XP_005265845.1 | ||
CEP135 | XM_011534412.2 | c.-58+3342A>G | intron_variant | Intron 1 of 15 | XP_011532714.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00255 AC: 388AN: 152192Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000785 AC: 195AN: 248494 AF XY: 0.000604 show subpopulations
GnomAD4 exome AF: 0.000250 AC: 365AN: 1458046Hom.: 1 Cov.: 30 AF XY: 0.000215 AC XY: 156AN XY: 725126 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00255 AC: 388AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.00243 AC XY: 181AN XY: 74460 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:4
- -
CEP135: BP4, BS1 -
- -
- -
not specified Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at