rs113013357
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_021254.4(CFAP298):c.630G>A(p.Lys210=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,614,180 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 Benign (★).
Frequency
Genomes: 𝑓 0.00087 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000062 ( 1 hom. )
Consequence
CFAP298
NM_021254.4 synonymous
NM_021254.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.347
Genes affected
CFAP298 (HGNC:1301): (cilia and flagella associated protein 298) This gene encodes a protein that plays a critical role in dynein arm assembly and motile cilia function. Mutations in this gene result in primary ciliary dyskinesia. Naturally occuring readthrough transcription occurs from this locus to the downstream t-complex 10 like (TCP10L) gene. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 21-32603197-C-T is Benign according to our data. Variant chr21-32603197-C-T is described in ClinVar as [Benign]. Clinvar id is 454927.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.347 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000873 (133/152312) while in subpopulation AFR AF= 0.00308 (128/41576). AF 95% confidence interval is 0.00264. There are 0 homozygotes in gnomad4. There are 57 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP298 | NM_021254.4 | c.630G>A | p.Lys210= | synonymous_variant | 5/7 | ENST00000290155.8 | |
CFAP298-TCP10L | NR_146638.2 | n.764G>A | non_coding_transcript_exon_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP298 | ENST00000290155.8 | c.630G>A | p.Lys210= | synonymous_variant | 5/7 | 1 | NM_021254.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000861 AC: 131AN: 152194Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000191 AC: 48AN: 251482Hom.: 1 AF XY: 0.000103 AC XY: 14AN XY: 135920
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GnomAD4 exome AF: 0.0000622 AC: 91AN: 1461868Hom.: 1 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727238
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GnomAD4 genome ? AF: 0.000873 AC: 133AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000765 AC XY: 57AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 26, 2023 | - - |
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