rs541219767
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The ENST00000316724.10(BIN1):c.1264-5A>C 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 0.0000318 in 1,571,182 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000316724.10 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BIN1 | NM_139343.3 | c.1264-5A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000316724.10 | NP_647593.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BIN1 | ENST00000316724.10 | c.1264-5A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_139343.3 | ENSP00000316779 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151604Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000866 AC: 15AN: 173172Hom.: 0 AF XY: 0.0000746 AC XY: 7AN XY: 93894
GnomAD4 exome AF: 0.0000232 AC: 33AN: 1419458Hom.: 0 Cov.: 31 AF XY: 0.0000256 AC XY: 18AN XY: 702116
GnomAD4 genome AF: 0.000112 AC: 17AN: 151724Hom.: 0 Cov.: 34 AF XY: 0.0000944 AC XY: 7AN XY: 74156
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 26, 2021 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. - |
Myopathy, centronuclear, 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at