chr11-66701629-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_ModerateBP6_Very_StrongBS1
The NM_006946.4(SPTBN2):c.2771C>A(p.Pro924Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000147 in 1,613,970 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P924L) has been classified as Uncertain significance.
Frequency
Consequence
NM_006946.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTBN2 | NM_006946.4 | c.2771C>A | p.Pro924Gln | missense_variant | 16/38 | ENST00000533211.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN2 | ENST00000533211.6 | c.2771C>A | p.Pro924Gln | missense_variant | 16/38 | 5 | NM_006946.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000480 AC: 73AN: 152092Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251474Hom.: 1 AF XY: 0.0000809 AC XY: 11AN XY: 135916
GnomAD4 exome AF: 0.000113 AC: 165AN: 1461878Hom.: 1 Cov.: 35 AF XY: 0.000103 AC XY: 75AN XY: 727242
GnomAD4 genome AF: 0.000480 AC: 73AN: 152092Hom.: 1 Cov.: 31 AF XY: 0.000512 AC XY: 38AN XY: 74284
ClinVar
Submissions by phenotype
SPTBN2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 24, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 24, 2016 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at