chr4-121843997-T-C
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 2P and 12B. PP2PP3BP4_StrongBS1BS2
The NM_176824.3(BBS7):c.1235A>G(p.Asp412Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00201 in 1,584,246 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D412Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_176824.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Benign. The variant received -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BBS7 | ENST00000264499.9 | c.1235A>G | p.Asp412Gly | missense_variant | Exon 12 of 19 | 1 | NM_176824.3 | ENSP00000264499.4 | ||
BBS7 | ENST00000506636.1 | c.1235A>G | p.Asp412Gly | missense_variant | Exon 12 of 18 | 1 | ENSP00000423626.1 |
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 223AN: 152060Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00149 AC: 334AN: 224248 AF XY: 0.00146 show subpopulations
GnomAD4 exome AF: 0.00207 AC: 2967AN: 1432068Hom.: 4 Cov.: 26 AF XY: 0.00202 AC XY: 1439AN XY: 711796 show subpopulations
GnomAD4 genome AF: 0.00147 AC: 223AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.00128 AC XY: 95AN XY: 74406 show subpopulations
ClinVar
Submissions by phenotype
not provided Uncertain:2
BBS7: PP3 -
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported in the heterozygous state in a patient with retinal dystrophy, postaxial polydactyly, and intellectual disability who also harbored a homozgyous variant in the BBS1 gene (Perea-Romero et al., 2022); This variant is associated with the following publications: (PMID: 25533962, 31376382, 35835773) -
Bardet-Biedl syndrome 7 Uncertain:1
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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Retinal dystrophy Uncertain:1
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BBS7-related ciliopathy Benign:1
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Bardet-Biedl syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at