rs375785879
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024649.5(BBS1):c.1110+45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000338 in 1,608,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00036 ( 0 hom. )
Consequence
BBS1
NM_024649.5 intron
NM_024649.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.88
Genes affected
BBS1 (HGNC:966): (Bardet-Biedl syndrome 1) Mutations in this gene have been observed in patients with the major form (type 1) of Bardet-Biedl syndrome. The encoded protein may play a role in eye, limb, cardiac and reproductive system development. [provided by RefSeq, Jul 2008]
ZDHHC24 (HGNC:27387): (zinc finger DHHC-type containing 24) Predicted to enable protein-cysteine S-palmitoyltransferase activity. Predicted to be involved in peptidyl-L-cysteine S-palmitoylation and protein targeting to membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BP6
Variant 11-66523927-C-T is Benign according to our data. Variant chr11-66523927-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 261746.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BBS1 | NM_024649.5 | c.1110+45C>T | intron_variant | ENST00000318312.12 | NP_078925.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BBS1 | ENST00000318312.12 | c.1110+45C>T | intron_variant | 1 | NM_024649.5 | ENSP00000317469.7 | ||||
ENSG00000256349 | ENST00000419755.3 | c.1221+45C>T | intron_variant | 2 | ENSP00000398526.3 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152204Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000199 AC: 49AN: 245660Hom.: 0 AF XY: 0.000180 AC XY: 24AN XY: 133442
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GnomAD4 exome AF: 0.000360 AC: 525AN: 1456360Hom.: 0 Cov.: 30 AF XY: 0.000346 AC XY: 251AN XY: 724710
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GnomAD4 genome AF: 0.000118 AC: 18AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74476
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at