chr6-159907599-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002377.4(MAS1):c.644G>A(p.Arg215Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,550 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_002377.4 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 |
---|---|---|---|---|---|---|---|
MAS1 | NM_002377.4 | c.644G>A | p.Arg215Gln | missense_variant | 3/3 | ENST00000674077.2 | |
MAS1 | NM_001366704.2 | c.644G>A | p.Arg215Gln | missense_variant | 2/2 | ||
MAS1 | XM_047418776.1 | c.644G>A | p.Arg215Gln | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAS1 | ENST00000674077.2 | c.644G>A | p.Arg215Gln | missense_variant | 3/3 | NM_002377.4 | P1 | ||
MAS1 | ENST00000252660.5 | c.644G>A | p.Arg215Gln | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151560Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251278Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135790
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461874Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727234
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151676Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2AN XY: 74130
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.644G>A (p.R215Q) alteration is located in exon 1 (coding exon 1) of the MAS1 gene. This alteration results from a G to A substitution at nucleotide position 644, causing the arginine (R) at amino acid position 215 to be replaced by a glutamine (Q). 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