19-47673720-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001394372.1(BICRA):āc.42T>Cā(p.Cys14=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,612,658 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 (ā ).
Frequency
Consequence
NM_001394372.1 splice_region, synonymous
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BICRA | NM_001394372.1 | c.42T>C | p.Cys14= | splice_region_variant, synonymous_variant | 4/15 | ENST00000594866.3 | NP_001381301.1 | |
BICRA | NM_015711.3 | c.42T>C | p.Cys14= | splice_region_variant, synonymous_variant | 4/15 | NP_056526.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BICRA | ENST00000594866.3 | c.42T>C | p.Cys14= | splice_region_variant, synonymous_variant | 4/15 | 2 | NM_001394372.1 | ENSP00000469738 | P2 | |
ENST00000599924.1 | n.87-58345T>C | intron_variant, non_coding_transcript_variant | 5 | |||||||
BICRA | ENST00000396720.7 | c.42T>C | p.Cys14= | splice_region_variant, synonymous_variant | 4/15 | 5 | ENSP00000379946 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000857 AC: 13AN: 151660Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000189 AC: 47AN: 248854Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135220
GnomAD4 exome AF: 0.000179 AC: 261AN: 1460998Hom.: 0 Cov.: 32 AF XY: 0.000183 AC XY: 133AN XY: 726840
GnomAD4 genome AF: 0.0000857 AC: 13AN: 151660Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2AN XY: 74048
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2023 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at