11-18933890-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001393578.1(MRGPRX1):c.895T>C(p.Ser299Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,610,670 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 Likely benign (★).
Frequency
Consequence
NM_001393578.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRGPRX1 | NM_001393578.1 | c.895T>C | p.Ser299Pro | missense_variant | 2/2 | ENST00000526914.2 | |
MRGPRX1 | NM_147199.4 | c.895T>C | p.Ser299Pro | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRGPRX1 | ENST00000526914.2 | c.895T>C | p.Ser299Pro | missense_variant | 2/2 | 3 | NM_001393578.1 | P1 | |
MRGPRX1 | ENST00000302797.4 | c.895T>C | p.Ser299Pro | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000106 AC: 16AN: 151304Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250712Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135552
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1459248Hom.: 0 Cov.: 31 AF XY: 0.0000455 AC XY: 33AN XY: 725942
GnomAD4 genome ? AF: 0.000106 AC: 16AN: 151422Hom.: 0 Cov.: 35 AF XY: 0.0000541 AC XY: 4AN XY: 74004
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at