rs62638716
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 3P and 20B. PM1PP2BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000318560.6(ABL1):c.1418G>A(p.Arg473Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000506 in 1,614,130 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R473G) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000318560.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABL1 | NM_005157.6 | c.1418G>A | p.Arg473Gln | missense_variant | 8/11 | ENST00000318560.6 | NP_005148.2 | |
ABL1 | NM_007313.3 | c.1475G>A | p.Arg492Gln | missense_variant | 8/11 | NP_009297.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABL1 | ENST00000318560.6 | c.1418G>A | p.Arg473Gln | missense_variant | 8/11 | 1 | NM_005157.6 | ENSP00000323315 | ||
ABL1 | ENST00000372348.9 | c.1475G>A | p.Arg492Gln | missense_variant | 8/11 | 1 | ENSP00000361423 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00281 AC: 428AN: 152202Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000633 AC: 159AN: 251358Hom.: 0 AF XY: 0.000442 AC XY: 60AN XY: 135862
GnomAD4 exome AF: 0.000267 AC: 390AN: 1461810Hom.: 2 Cov.: 31 AF XY: 0.000234 AC XY: 170AN XY: 727206
GnomAD4 genome AF: 0.00280 AC: 427AN: 152320Hom.: 1 Cov.: 32 AF XY: 0.00258 AC XY: 192AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 27, 2023 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
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