rs2083437
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173519.3(CLVS1):c.631-36676G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,080 control chromosomes in the GnomAD database, including 2,879 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.11 ( 2879 hom., cov: 32)
Consequence
CLVS1
NM_173519.3 intron
NM_173519.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.597
Genes affected
CLVS1 (HGNC:23139): (clavesin 1) Enables phosphatidylinositol-3,5-bisphosphate binding activity. Predicted to be involved in lysosome organization. Located in endosome. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLVS1 | NM_173519.3 | c.631-36676G>C | intron_variant | ENST00000325897.5 | NP_775790.1 | |||
CLVS1 | XM_017013141.2 | c.631-36676G>C | intron_variant | XP_016868630.1 | ||||
CLVS1 | XM_017013142.3 | c.631-36676G>C | intron_variant | XP_016868631.1 | ||||
CLVS1 | XM_024447079.2 | c.631-36676G>C | intron_variant | XP_024302847.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLVS1 | ENST00000325897.5 | c.631-36676G>C | intron_variant | 1 | NM_173519.3 | ENSP00000325506.4 |
Frequencies
GnomAD3 genomes AF: 0.110 AC: 16764AN: 151962Hom.: 2880 Cov.: 32
GnomAD3 genomes
AF:
AC:
16764
AN:
151962
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.110 AC: 16795AN: 152080Hom.: 2879 Cov.: 32 AF XY: 0.108 AC XY: 8019AN XY: 74336
GnomAD4 genome
AF:
AC:
16795
AN:
152080
Hom.:
Cov.:
32
AF XY:
AC XY:
8019
AN XY:
74336
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
199
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at