chr8-66566232-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001080416.4(MYBL1):c.1962A>T(p.Arg654Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000289 in 1,471,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYBL1 | NM_001080416.4 | c.1962A>T | p.Arg654Ser | missense_variant | 15/16 | ENST00000522677.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBL1 | ENST00000522677.8 | c.1962A>T | p.Arg654Ser | missense_variant | 15/16 | 1 | NM_001080416.4 | A1 | |
MYBL1 | ENST00000524176.2 | c.1950+452A>T | intron_variant | 1 | P4 | ||||
MYBL1 | ENST00000517885.5 | c.936A>T | p.Arg312Ser | missense_variant | 11/12 | 5 | |||
MYBL1 | ENST00000522419.1 | n.188+452A>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152022Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000176 AC: 23AN: 130524Hom.: 0 AF XY: 0.000145 AC XY: 10AN XY: 69064
GnomAD4 exome AF: 0.000306 AC: 404AN: 1319686Hom.: 0 Cov.: 24 AF XY: 0.000265 AC XY: 173AN XY: 653718
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152022Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.1962A>T (p.R654S) alteration is located in exon 15 (coding exon 15) of the MYBL1 gene. This alteration results from a A to T substitution at nucleotide position 1962, causing the arginine (R) at amino acid position 654 to be replaced by a serine (S). 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