rs2229067
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_005157.6(ABL1):c.2915C>T(p.Ser972Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0185 in 1,613,586 control chromosomes in the GnomAD database, including 437 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S972P) has been classified as Uncertain significance.
Frequency
Consequence
NM_005157.6 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
ABL1 | NM_005157.6 | c.2915C>T | p.Ser972Leu | missense_variant | 11/11 | ENST00000318560.6 | |
ABL1 | NM_007313.3 | c.2972C>T | p.Ser991Leu | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABL1 | ENST00000318560.6 | c.2915C>T | p.Ser972Leu | missense_variant | 11/11 | 1 | NM_005157.6 | ||
ABL1 | ENST00000372348.9 | c.2972C>T | p.Ser991Leu | missense_variant | 11/11 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0279 AC: 4247AN: 152214Hom.: 87 Cov.: 33
GnomAD3 exomes AF: 0.0210 AC: 5260AN: 250232Hom.: 93 AF XY: 0.0203 AC XY: 2756AN XY: 135534
GnomAD4 exome AF: 0.0175 AC: 25636AN: 1461254Hom.: 350 Cov.: 32 AF XY: 0.0173 AC XY: 12553AN XY: 726944
GnomAD4 genome AF: 0.0279 AC: 4250AN: 152332Hom.: 87 Cov.: 33 AF XY: 0.0291 AC XY: 2164AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at