rs201034280
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_080860.4(RSPH1):c.501+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00281 in 1,613,966 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_080860.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSPH1 | NM_080860.4 | c.501+7C>T | splice_region_variant, intron_variant | ENST00000291536.8 | |||
RSPH1 | NM_001286506.2 | c.387+7C>T | splice_region_variant, intron_variant | ||||
RSPH1 | XM_005261208.3 | c.294+7C>T | splice_region_variant, intron_variant | ||||
RSPH1 | XM_011529786.2 | c.501+7C>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPH1 | ENST00000291536.8 | c.501+7C>T | splice_region_variant, intron_variant | 1 | NM_080860.4 | P1 | |||
RSPH1 | ENST00000398352.3 | c.387+7C>T | splice_region_variant, intron_variant | 5 | |||||
RSPH1 | ENST00000493019.1 | n.1134C>T | non_coding_transcript_exon_variant | 4/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00175 AC: 267AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00200 AC: 504AN: 251390Hom.: 3 AF XY: 0.00208 AC XY: 282AN XY: 135856
GnomAD4 exome AF: 0.00292 AC: 4267AN: 1461814Hom.: 13 Cov.: 30 AF XY: 0.00277 AC XY: 2018AN XY: 727222
GnomAD4 genome ? AF: 0.00175 AC: 267AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.00159 AC XY: 118AN XY: 74322
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | RSPH1: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at