chr9-130854093-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_005157.6(ABL1):āc.109T>Gā(p.Phe37Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,614,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005157.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABL1 | NM_005157.6 | c.109T>G | p.Phe37Val | missense_variant | 2/11 | ENST00000318560.6 | NP_005148.2 | |
ABL1 | NM_007313.3 | c.166T>G | p.Phe56Val | missense_variant | 2/11 | NP_009297.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABL1 | ENST00000318560.6 | c.109T>G | p.Phe37Val | missense_variant | 2/11 | 1 | NM_005157.6 | ENSP00000323315 | ||
ABL1 | ENST00000372348.9 | c.166T>G | p.Phe56Val | missense_variant | 2/11 | 1 | ENSP00000361423 | P1 | ||
ABL1 | ENST00000393293.4 | c.163T>G | p.Phe55Val | missense_variant | 2/2 | 5 | ENSP00000376971 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461810Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727206
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74482
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 24, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ABL1 protein function. This sequence change replaces phenylalanine with valine at codon 56 of the ABL1 protein (p.Phe56Val). The phenylalanine residue is moderately conserved and there is a small physicochemical difference between phenylalanine and valine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with ABL1-related conditions. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at