5-54456136-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP3BP4_ModerateBP6_Very_StrongBS2
The NM_006308.3(HSPB3):c.347G>A(p.Arg116Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000206 in 1,614,102 control chromosomes in the GnomAD database, including 3 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. R116P) has been classified as Likely benign.
Frequency
Consequence
NM_006308.3 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 |
---|---|---|---|---|---|---|---|
HSPB3 | NM_006308.3 | c.347G>A | p.Arg116Gln | missense_variant | 1/1 | ENST00000302005.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPB3 | ENST00000302005.3 | c.347G>A | p.Arg116Gln | missense_variant | 1/1 | NM_006308.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000990 AC: 249AN: 251412Hom.: 2 AF XY: 0.000670 AC XY: 91AN XY: 135882
GnomAD4 exome AF: 0.000214 AC: 313AN: 1461856Hom.: 3 Cov.: 53 AF XY: 0.000169 AC XY: 123AN XY: 727240
GnomAD4 genome AF: 0.000131 AC: 20AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 28, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 09, 2017 | - - |
Neuronopathy, distal hereditary motor, type 2C Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at