chr11-66690210-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_006946.4(SPTBN2):c.5639G>A(p.Arg1880His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 1,613,734 control chromosomes in the GnomAD database, including 460 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. R1880C) 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 -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTBN2 | NM_006946.4 | c.5639G>A | p.Arg1880His | missense_variant | 28/38 | ENST00000533211.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN2 | ENST00000533211.6 | c.5639G>A | p.Arg1880His | missense_variant | 28/38 | 5 | NM_006946.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0159 AC: 2425AN: 152242Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.0168 AC: 4135AN: 246366Hom.: 46 AF XY: 0.0176 AC XY: 2348AN XY: 133632
GnomAD4 exome AF: 0.0226 AC: 32975AN: 1461374Hom.: 441 Cov.: 32 AF XY: 0.0223 AC XY: 16196AN XY: 727022
GnomAD4 genome ? AF: 0.0159 AC: 2419AN: 152360Hom.: 19 Cov.: 32 AF XY: 0.0152 AC XY: 1136AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 12, 2017 | - - |
Autosomal dominant cerebellar ataxia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at