chr8-67064428-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001364869.1(CSPP1):āc.30A>Gā(p.Val10Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00693 in 1,613,876 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001364869.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSPP1 | NM_001382391.1 | c.-121A>G | 5_prime_UTR_variant | Exon 1 of 31 | ENST00000678616.1 | NP_001369320.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSPP1 | ENST00000678616 | c.-121A>G | 5_prime_UTR_variant | Exon 1 of 31 | NM_001382391.1 | ENSP00000504733.1 |
Frequencies
GnomAD3 genomes AF: 0.00462 AC: 703AN: 152132Hom.: 5 Cov.: 31
GnomAD3 exomes AF: 0.00466 AC: 1159AN: 248848Hom.: 6 AF XY: 0.00443 AC XY: 598AN XY: 135114
GnomAD4 exome AF: 0.00717 AC: 10480AN: 1461628Hom.: 41 Cov.: 31 AF XY: 0.00699 AC XY: 5085AN XY: 727154
GnomAD4 genome AF: 0.00461 AC: 702AN: 152248Hom.: 5 Cov.: 31 AF XY: 0.00410 AC XY: 305AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent, not in splice consensus -
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CSPP1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Joubert syndrome 21 Benign:1
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not provided Benign:1
CSPP1: BP4, BP7, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at