chr9-130884916-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP6_ModerateBS1
The NM_005157.6(ABL1):c.2626A>G(p.Arg876Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,611,432 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R876W) has been classified as Uncertain significance.
Frequency
Consequence
NM_005157.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABL1 | NM_005157.6 | c.2626A>G | p.Arg876Gly | missense_variant | 11/11 | ENST00000318560.6 | |
ABL1 | NM_007313.3 | c.2683A>G | p.Arg895Gly | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABL1 | ENST00000318560.6 | c.2626A>G | p.Arg876Gly | missense_variant | 11/11 | 1 | NM_005157.6 | ||
ABL1 | ENST00000372348.9 | c.2683A>G | p.Arg895Gly | missense_variant | 11/11 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000839 AC: 2AN: 238338Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 131048
GnomAD4 exome AF: 0.0000528 AC: 77AN: 1459276Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 39AN XY: 725844
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 05, 2022 | - - |
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