6-159907611-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002377.4(MAS1):āc.656G>Cā(p.Trp219Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,588 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 (ā ).
Frequency
Consequence
NM_002377.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAS1 | NM_002377.4 | c.656G>C | p.Trp219Ser | missense_variant | 3/3 | ENST00000674077.2 | |
MAS1 | NM_001366704.2 | c.656G>C | p.Trp219Ser | missense_variant | 2/2 | ||
MAS1 | XM_047418776.1 | c.656G>C | p.Trp219Ser | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAS1 | ENST00000674077.2 | c.656G>C | p.Trp219Ser | missense_variant | 3/3 | NM_002377.4 | P1 | ||
MAS1 | ENST00000252660.5 | c.656G>C | p.Trp219Ser | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000152 AC: 23AN: 151598Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251322Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135820
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461872Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727234
GnomAD4 genome AF: 0.000152 AC: 23AN: 151716Hom.: 0 Cov.: 30 AF XY: 0.000175 AC XY: 13AN XY: 74166
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.656G>C (p.W219S) alteration is located in exon 1 (coding exon 1) of the MAS1 gene. This alteration results from a G to C substitution at nucleotide position 656, causing the tryptophan (W) at amino acid position 219 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