chr8-66573484-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001080416.4(MYBL1):āc.1493A>Gā(p.Asn498Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000404 in 1,607,452 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.1493A>G | p.Asn498Ser | missense_variant | 11/16 | ENST00000522677.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBL1 | ENST00000522677.8 | c.1493A>G | p.Asn498Ser | missense_variant | 11/16 | 1 | NM_001080416.4 | A1 | |
MYBL1 | ENST00000524176.2 | c.1493A>G | p.Asn498Ser | missense_variant | 11/15 | 1 | P4 | ||
MYBL1 | ENST00000517885.5 | c.467A>G | p.Asn156Ser | missense_variant | 7/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000370 AC: 9AN: 243422Hom.: 0 AF XY: 0.0000303 AC XY: 4AN XY: 132056
GnomAD4 exome AF: 0.0000241 AC: 35AN: 1455274Hom.: 0 Cov.: 30 AF XY: 0.0000180 AC XY: 13AN XY: 723590
GnomAD4 genome AF: 0.000197 AC: 30AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.1493A>G (p.N498S) 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 1493, causing the asparagine (N) at amino acid position 498 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