rs10097570
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040032.2(C8orf74):c.242-6251T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 181,272 control chromosomes in the GnomAD database, including 6,989 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 6395 hom., cov: 33)
Exomes 𝑓: 0.094 ( 594 hom. )
Consequence
C8orf74
NM_001040032.2 intron
NM_001040032.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.87
Genes affected
C8orf74 (HGNC:32296): (chromosome 8 open reading frame 74)
RP1L1 (HGNC:15946): (RP1 like 1) This gene encodes a member of the doublecortin family. The protein encoded by this gene contains two N-terminal doublecortin domains, which bind microtubules and regulate microtubule polymerization, and two C-terminal large repetitive regions, both of which contain a high percentage of glutamine and glutamic acid residues. This protein is a retinal-specific protein. Its exact length varies among individuals due to the presence of a 16aa repeat in the first C-terminal repetitive region. The 16aa repeat is encoded by the highly polymorphic 48-bp repeat, and 1-6 copies of the 16aa repeat have been identified in normal individuals. The current reference sequence shown here has a single copy of the 16aa repeat. This protein and the RP1 protein, another retinal-specific protein, play essential and synergistic roles in affecting photosensitivity and outer segment morphogenesis of rod photoreceptors. Mutations in this gene cause occult macular dystrophy (OMD). [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C8orf74 | NM_001040032.2 | c.242-6251T>G | intron_variant | ENST00000304519.10 | |||
C8orf74 | XM_047421493.1 | c.299-6251T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C8orf74 | ENST00000304519.10 | c.242-6251T>G | intron_variant | 1 | NM_001040032.2 | P1 | |||
C8orf74 | ENST00000521818.1 | c.*417T>G | 3_prime_UTR_variant | 3/3 | 5 | ||||
C8orf74 | ENST00000523289.5 | c.*133+4077T>G | intron_variant, NMD_transcript_variant | 2 | |||||
RP1L1 | ENST00000329335.3 | n.231+20609A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.170 AC: 25804AN: 151998Hom.: 6366 Cov.: 33
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GnomAD4 exome AF: 0.0937 AC: 2733AN: 29156Hom.: 594 Cov.: 0 AF XY: 0.0840 AC XY: 1294AN XY: 15404
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GnomAD4 genome ? AF: 0.170 AC: 25889AN: 152116Hom.: 6395 Cov.: 33 AF XY: 0.168 AC XY: 12486AN XY: 74382
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ClinVar
Not reported inComputational 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