rs149412304
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_ModerateBP6_Very_StrongBS2
The NM_005157.6(ABL1):c.2416C>A(p.Pro806Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000211 in 1,612,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. P806L) 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.2416C>A | p.Pro806Thr | missense_variant | 11/11 | ENST00000318560.6 | |
ABL1 | NM_007313.3 | c.2473C>A | p.Pro825Thr | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABL1 | ENST00000318560.6 | c.2416C>A | p.Pro806Thr | missense_variant | 11/11 | 1 | NM_005157.6 | ||
ABL1 | ENST00000372348.9 | c.2473C>A | p.Pro825Thr | missense_variant | 11/11 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000448 AC: 11AN: 245778Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134326
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1460388Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726478
GnomAD4 genome AF: 0.000131 AC: 20AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74474
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 02, 2023 | - - |
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