rs201897299
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001540.5(HSPB1):c.365-7C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,610,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_001540.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPB1 | NM_001540.5 | c.365-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000248553.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPB1 | ENST00000248553.7 | c.365-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001540.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000119 AC: 18AN: 151870Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000149 AC: 37AN: 248724Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135280
GnomAD4 exome AF: 0.000121 AC: 177AN: 1458776Hom.: 0 Cov.: 32 AF XY: 0.000106 AC XY: 77AN XY: 725706
GnomAD4 genome ? AF: 0.000119 AC: 18AN: 151870Hom.: 0 Cov.: 32 AF XY: 0.0000809 AC XY: 6AN XY: 74172
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, London Health Sciences Centre | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 23, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Charcot-Marie-Tooth disease axonal type 2F Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at