rs587778015
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The ENST00000318560.6(ABL1):c.2930G>A(p.Ser977Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,588 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. S977R) has been classified as Likely benign.
Frequency
Consequence
ENST00000318560.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABL1 | NM_005157.6 | c.2930G>A | p.Ser977Asn | missense_variant | 11/11 | ENST00000318560.6 | NP_005148.2 | |
ABL1 | NM_007313.3 | c.2987G>A | p.Ser996Asn | missense_variant | 11/11 | NP_009297.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABL1 | ENST00000318560.6 | c.2930G>A | p.Ser977Asn | missense_variant | 11/11 | 1 | NM_005157.6 | ENSP00000323315 | ||
ABL1 | ENST00000372348.9 | c.2987G>A | p.Ser996Asn | missense_variant | 11/11 | 1 | ENSP00000361423 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250406Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135578
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461388Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727026
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 11, 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