rs10027479
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_152618.3(BBS12):āc.1381A>Cā(p.Asn461His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00423 in 1,614,222 control chromosomes in the GnomAD database, including 255 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_152618.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BBS12 | NM_152618.3 | c.1381A>C | p.Asn461His | missense_variant | 2/2 | ENST00000314218.8 | NP_689831.2 | |
BBS12 | NM_001178007.2 | c.1381A>C | p.Asn461His | missense_variant | 3/3 | NP_001171478.1 | ||
BBS12 | XM_011531680.3 | c.1381A>C | p.Asn461His | missense_variant | 2/2 | XP_011529982.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BBS12 | ENST00000314218.8 | c.1381A>C | p.Asn461His | missense_variant | 2/2 | 1 | NM_152618.3 | ENSP00000319062 | P1 | |
BBS12 | ENST00000542236.5 | c.1381A>C | p.Asn461His | missense_variant | 3/3 | 2 | ENSP00000438273 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0232 AC: 3528AN: 152218Hom.: 135 Cov.: 33
GnomAD3 exomes AF: 0.00591 AC: 1487AN: 251466Hom.: 58 AF XY: 0.00435 AC XY: 591AN XY: 135906
GnomAD4 exome AF: 0.00225 AC: 3288AN: 1461886Hom.: 119 Cov.: 64 AF XY: 0.00198 AC XY: 1438AN XY: 727242
GnomAD4 genome AF: 0.0232 AC: 3537AN: 152336Hom.: 136 Cov.: 33 AF XY: 0.0228 AC XY: 1697AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:3Other:1
not provided, no classification provided | literature only | NEI Ophthalmic Genomics Laboratory, National Institutes of Health | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | This variant is associated with the following publications: (PMID: 20498079, 22025579, 27884173, 27894351) - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 30, 2017 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 05, 2016 | - - |
Bardet-Biedl syndrome 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Dec 15, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
Bardet-Biedl syndrome 12 Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Bardet-Biedl syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at