rs762169661
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_003611.3(OFD1):c.282C>T(p.Phe94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,207,344 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000054 ( 0 hom., 3 hem., cov: 22)
Exomes 𝑓: 0.000012 ( 0 hom. 4 hem. )
Consequence
OFD1
NM_003611.3 synonymous
NM_003611.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.44
Genes affected
OFD1 (HGNC:2567): (OFD1 centriole and centriolar satellite protein) This gene is located on the X chromosome and encodes a centrosomal protein. A knockout mouse model has been used to study the effect of mutations in this gene. The mouse gene is also located on the X chromosome, however, unlike the human gene it is not subject to X inactivation. Mutations in this gene are associated with oral-facial-digital syndrome type I and Simpson-Golabi-Behmel syndrome type 2. Many pseudogenes have been identified; a single pseudogene is found on chromosome 5 while as many as fifteen have been found on the Y chromosome. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
?
Variant X-13736648-C-T is Benign according to our data. Variant chrX-13736648-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 412873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=2.44 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OFD1 | NM_003611.3 | c.282C>T | p.Phe94= | synonymous_variant | 3/23 | ENST00000340096.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OFD1 | ENST00000340096.11 | c.282C>T | p.Phe94= | synonymous_variant | 3/23 | 1 | NM_003611.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000540 AC: 6AN: 111171Hom.: 0 Cov.: 22 AF XY: 0.0000899 AC XY: 3AN XY: 33355
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GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183378Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67826
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GnomAD4 exome AF: 0.0000119 AC: 13AN: 1096173Hom.: 0 Cov.: 29 AF XY: 0.0000111 AC XY: 4AN XY: 361577
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GnomAD4 genome ? AF: 0.0000540 AC: 6AN: 111171Hom.: 0 Cov.: 22 AF XY: 0.0000899 AC XY: 3AN XY: 33355
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Familial aplasia of the vermis;C1510460:Orofaciodigital syndrome I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 09, 2023 | - - |
Retinitis pigmentosa 23;C1510460:Orofaciodigital syndrome I;C1846175:Simpson-Golabi-Behmel syndrome type 2;C2749019:Joubert syndrome 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 17, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at