19-48796507-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001190.4(BCAT2):c.1066-5C>A 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 0.000131 in 1,612,658 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_001190.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAT2 | NM_001190.4 | c.1066-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000316273.11 | |||
BCAT2 | NM_001164773.2 | c.790-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
BCAT2 | NM_001284325.2 | c.946-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAT2 | ENST00000316273.11 | c.1066-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001190.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000184 AC: 46AN: 249624Hom.: 0 AF XY: 0.000193 AC XY: 26AN XY: 134988
GnomAD4 exome AF: 0.000129 AC: 189AN: 1460486Hom.: 1 Cov.: 33 AF XY: 0.000125 AC XY: 91AN XY: 726580
GnomAD4 genome AF: 0.000145 AC: 22AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74328
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at