8-66573419-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001080416.4(MYBL1):c.1558A>G(p.Ile520Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,056 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 Uncertain significance (★).
Frequency
Consequence
NM_001080416.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYBL1 | NM_001080416.4 | c.1558A>G | p.Ile520Val | missense_variant | 11/16 | ENST00000522677.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBL1 | ENST00000522677.8 | c.1558A>G | p.Ile520Val | missense_variant | 11/16 | 1 | NM_001080416.4 | A1 | |
MYBL1 | ENST00000524176.2 | c.1558A>G | p.Ile520Val | missense_variant | 11/15 | 1 | P4 | ||
MYBL1 | ENST00000517885.5 | c.532A>G | p.Ile178Val | missense_variant | 7/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248298Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134684
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460730Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 726596
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2024 | The c.1558A>G (p.I520V) alteration is located in exon 11 (coding exon 11) of the MYBL1 gene. This alteration results from a A to G substitution at nucleotide position 1558, causing the isoleucine (I) at amino acid position 520 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at