chr17-78222827-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000587746.5(BIRC5):c.341-1G>A variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00723 in 1,536,050 control chromosomes in the GnomAD database, including 54 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 Likely benign (★).
Frequency
Consequence
ENST00000587746.5 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BIRC5 | NM_001168.3 | c.340-638G>A | intron_variant | ENST00000350051.8 | |||
BIRC5 | NM_001012270.2 | c.222-638G>A | intron_variant | ||||
BIRC5 | NM_001012271.2 | c.409-638G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BIRC5 | ENST00000350051.8 | c.340-638G>A | intron_variant | 1 | NM_001168.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00591 AC: 900AN: 152162Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00491 AC: 661AN: 134524Hom.: 3 AF XY: 0.00498 AC XY: 365AN XY: 73274
GnomAD4 exome AF: 0.00738 AC: 10213AN: 1383770Hom.: 50 Cov.: 32 AF XY: 0.00727 AC XY: 4964AN XY: 682832
GnomAD4 genome ? AF: 0.00591 AC: 900AN: 152280Hom.: 4 Cov.: 33 AF XY: 0.00559 AC XY: 416AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | BIRC5: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at