7-33129748-T-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_198428.3(BBS9):c.-305T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00542 in 152,668 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0054 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 0 hom. )
Consequence
BBS9
NM_198428.3 5_prime_UTR
NM_198428.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.598
Genes affected
BBS9 (HGNC:30000): (Bardet-Biedl syndrome 9) This gene is downregulated by parathyroid hormone in osteoblastic cells, and therefore is thought to be involved in parathyroid hormone action in bones. The exact function of this gene has not yet been determined. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 7-33129748-T-G is Benign according to our data. Variant chr7-33129748-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 360053.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency = 0.0625 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BBS9 | NM_198428.3 | c.-305T>G | 5_prime_UTR_variant | 1/23 | ENST00000242067.11 | NP_940820.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BBS9 | ENST00000242067.11 | c.-305T>G | 5_prime_UTR_variant | 1/23 | 1 | NM_198428.3 | ENSP00000242067 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00541 AC: 823AN: 151992Hom.: 9 Cov.: 32
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GnomAD4 exome AF: 0.00179 AC: 1AN: 558Hom.: 0 Cov.: 0 AF XY: 0.00231 AC XY: 1AN XY: 432
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GnomAD4 genome AF: 0.00544 AC: 827AN: 152110Hom.: 9 Cov.: 32 AF XY: 0.00562 AC XY: 418AN XY: 74330
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Bardet-Biedl syndrome 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
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BayesDel_noAF
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