rs121913461
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP2PP3_ModeratePP5
The NM_005157.6(ABL1):c.757T>C(p.Tyr253His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y253F) has been classified as Likely pathogenic.
Frequency
Consequence
NM_005157.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABL1 | NM_005157.6 | c.757T>C | p.Tyr253His | missense_variant | 4/11 | ENST00000318560.6 | |
ABL1 | NM_007313.3 | c.814T>C | p.Tyr272His | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABL1 | ENST00000318560.6 | c.757T>C | p.Tyr253His | missense_variant | 4/11 | 1 | NM_005157.6 | ||
ABL1 | ENST00000372348.9 | c.814T>C | p.Tyr272His | missense_variant | 4/11 | 1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Chronic myelogenous leukemia, BCR-ABL1 positive Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Database of Curated Mutations (DoCM) | Jul 14, 2015 | - - |
Leukemia, Philadelphia chromosome-positive, resistant to imatinib Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 09, 2002 | - - |
Lymphoblastic leukemia, acute, with lymphomatous features Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Database of Curated Mutations (DoCM) | Jul 14, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at