21-42475879-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_080860.4(RSPH1):c.877+19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,608,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
RSPH1
NM_080860.4 intron
NM_080860.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.633
Genes affected
RSPH1 (HGNC:12371): (radial spoke head component 1) This gene encodes a male meiotic metaphase chromosome-associated acidic protein. This gene is expressed in tissues with motile cilia or flagella, including the trachea, lungs, airway brushings, and testes. Mutations in this gene result in primary ciliary dyskinesia-24. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 21-42475879-C-T is Benign according to our data. Variant chr21-42475879-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3691068.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RSPH1 | NM_080860.4 | c.877+19G>A | intron_variant | Intron 8 of 8 | ENST00000291536.8 | NP_543136.1 | ||
RSPH1 | NM_001286506.2 | c.763+19G>A | intron_variant | Intron 7 of 7 | NP_001273435.1 | |||
RSPH1 | XM_011529786.2 | c.805+19G>A | intron_variant | Intron 7 of 7 | XP_011528088.1 | |||
RSPH1 | XM_005261208.3 | c.670+19G>A | intron_variant | Intron 6 of 6 | XP_005261265.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RSPH1 | ENST00000291536.8 | c.877+19G>A | intron_variant | Intron 8 of 8 | 1 | NM_080860.4 | ENSP00000291536.3 | |||
RSPH1 | ENST00000398352.3 | c.763+19G>A | intron_variant | Intron 7 of 7 | 5 | ENSP00000381395.3 | ||||
RSPH1 | ENST00000493019.1 | n.2495+19G>A | intron_variant | Intron 7 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000204 AC: 3AN: 147218Hom.: 0 Cov.: 27
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GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461516Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727092
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GnomAD4 genome AF: 0.0000204 AC: 3AN: 147218Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 71336
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Mar 07, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at