rs369183561
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003611.3(OFD1):c.2996+25C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000916 in 1,124,935 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 31 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 0.000036 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000098 ( 0 hom. 30 hem. )
Consequence
OFD1
NM_003611.3 intron
NM_003611.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.330
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant X-13768810-C-G is Benign according to our data. Variant chrX-13768810-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 259099.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAdExome4 at 30 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OFD1 | NM_003611.3 | c.2996+25C>G | intron_variant | ENST00000340096.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OFD1 | ENST00000340096.11 | c.2996+25C>G | intron_variant | 1 | NM_003611.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000357 AC: 4AN: 111965Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34119
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GnomAD3 exomes AF: 0.0000819 AC: 15AN: 183172Hom.: 0 AF XY: 0.0000887 AC XY: 6AN XY: 67664
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GnomAD4 exome AF: 0.0000977 AC: 99AN: 1012970Hom.: 0 Cov.: 23 AF XY: 0.000102 AC XY: 30AN XY: 293840
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GnomAD4 genome ? AF: 0.0000357 AC: 4AN: 111965Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34119
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
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