rs142072750
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_080860.4(RSPH1):c.649T>C(p.Leu217=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,614,186 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L217L) has been classified as Likely benign.
Frequency
Consequence
NM_080860.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSPH1 | NM_080860.4 | c.649T>C | p.Leu217= | synonymous_variant | 7/9 | ENST00000291536.8 | |
RSPH1 | NM_001286506.2 | c.535T>C | p.Leu179= | synonymous_variant | 6/8 | ||
RSPH1 | XM_011529786.2 | c.577T>C | p.Leu193= | synonymous_variant | 6/8 | ||
RSPH1 | XM_005261208.3 | c.442T>C | p.Leu148= | synonymous_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPH1 | ENST00000291536.8 | c.649T>C | p.Leu217= | synonymous_variant | 7/9 | 1 | NM_080860.4 | P1 | |
RSPH1 | ENST00000398352.3 | c.535T>C | p.Leu179= | synonymous_variant | 6/8 | 5 | |||
RSPH1 | ENST00000493019.1 | n.2267T>C | non_coding_transcript_exon_variant | 6/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251394Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135906
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1461838Hom.: 1 Cov.: 34 AF XY: 0.0000509 AC XY: 37AN XY: 727214
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152348Hom.: 0 Cov.: 34 AF XY: 0.000175 AC XY: 13AN XY: 74492
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | RSPH1: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at