9-130854062-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PVS1_ModerateBP6_ModerateBS2
The NM_005157.6(ABL1):c.80-2A>G variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000811 in 1,602,226 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005157.6 splice_acceptor
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABL1 | NM_005157.6 | c.80-2A>G | splice_acceptor_variant | ENST00000318560.6 | NP_005148.2 | |||
ABL1 | NM_007313.3 | c.137-2A>G | splice_acceptor_variant | NP_009297.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABL1 | ENST00000318560.6 | c.80-2A>G | splice_acceptor_variant | 1 | NM_005157.6 | ENSP00000323315 | ||||
ABL1 | ENST00000372348.9 | c.137-2A>G | splice_acceptor_variant | 1 | ENSP00000361423 | P1 | ||||
ABL1 | ENST00000393293.4 | c.137-5A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000376971 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000290 AC: 7AN: 241714Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130520
GnomAD4 exome AF: 0.00000828 AC: 12AN: 1450130Hom.: 0 Cov.: 30 AF XY: 0.00000555 AC XY: 4AN XY: 720366
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74284
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 02, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at