chr11-66521261-TGTTTGCAGATG-T

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PVS1PM2PP3PP5_Very_Strong

The NM_024649.5(BBS1):​c.724-8_726del variant causes a splice acceptor, coding sequence, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: not found (cov: 32)

Consequence

BBS1
NM_024649.5 splice_acceptor, coding_sequence, intron

Scores

Not classified

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:3

Conservation

PhyloP100: 8.62
Variant links:
Genes affected
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]
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]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 19 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 6.4, offset of 20, new splice context is: cagcgtccccgtcttcctAGagg. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
Variant 11-66521261-TGTTTGCAGATG-T is Pathogenic according to our data. Variant chr11-66521261-TGTTTGCAGATG-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 865945.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BBS1NM_024649.5 linkuse as main transcriptc.724-8_726del splice_acceptor_variant, coding_sequence_variant, intron_variant 9/17 ENST00000318312.12
ZDHHC24NM_001348571.2 linkuse as main transcriptc.*216_*226del 3_prime_UTR_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BBS1ENST00000318312.12 linkuse as main transcriptc.724-8_726del splice_acceptor_variant, coding_sequence_variant, intron_variant 9/171 NM_024649.5 P1Q8NFJ9-1

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

BBS1-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesFeb 09, 2023The BBS1 c.724-8_726del11 variant is predicted to result in a deletion affecting a canonical splice site. This variant deletes the canonical splice acceptor site; an alternative splice acceptor is created that is predicted to introduce a frameshift (p.?). This variant has been reported in the compound heterozygous state with a well-established pathogenic variant in an individual with Bardet-Biedl syndrome (Billingsley et al. 2010. PubMed ID: 20472660; Grudzinska Pechhacker et al. 2021. PubMed ID: 34940782). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating it is rare. Frameshift variants in BBS1 are expected to be pathogenic. This variant is interpreted as pathogenic. -
Retinal dystrophy Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingBlueprint GeneticsJun 15, 2019- -
Bardet-Biedl syndrome Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 23, 2022For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 865945). This variant has been observed in individuals with clinical features of Bardet-Biedl syndrome (Invitae). This variant is not present in population databases (gnomAD no frequency). This variant results in the deletion of part of exon 9 (c.724-8_726del) of the BBS1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BBS1 are known to be pathogenic (PMID: 12118255, 21520335, 27032803). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1856202628; hg19: chr11-66288732; API