21-42475990-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080860.4(RSPH1):c.785T>A(p.Met262Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M262T) has been classified as Likely benign.
Frequency
Consequence
NM_080860.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSPH1 | NM_080860.4 | c.785T>A | p.Met262Lys | missense_variant | 8/9 | ENST00000291536.8 | |
RSPH1 | NM_001286506.2 | c.671T>A | p.Met224Lys | missense_variant | 7/8 | ||
RSPH1 | XM_011529786.2 | c.713T>A | p.Met238Lys | missense_variant | 7/8 | ||
RSPH1 | XM_005261208.3 | c.578T>A | p.Met193Lys | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPH1 | ENST00000291536.8 | c.785T>A | p.Met262Lys | missense_variant | 8/9 | 1 | NM_080860.4 | P1 | |
RSPH1 | ENST00000398352.3 | c.671T>A | p.Met224Lys | missense_variant | 7/8 | 5 | |||
RSPH1 | ENST00000493019.1 | n.2403T>A | non_coding_transcript_exon_variant | 7/8 | 2 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 28
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.