11-18934577-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001393578.1(MRGPRX1):c.208G>T(p.Ala70Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,609,520 control chromosomes in the GnomAD database, including 3 homozygotes. 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_001393578.1 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 |
---|---|---|---|---|---|---|---|
MRGPRX1 | NM_001393578.1 | c.208G>T | p.Ala70Ser | missense_variant | 2/2 | ENST00000526914.2 | |
MRGPRX1 | NM_147199.4 | c.208G>T | p.Ala70Ser | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRGPRX1 | ENST00000526914.2 | c.208G>T | p.Ala70Ser | missense_variant | 2/2 | 3 | NM_001393578.1 | P1 | |
MRGPRX1 | ENST00000302797.4 | c.208G>T | p.Ala70Ser | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000330 AC: 5AN: 151458Hom.: 1 Cov.: 35
GnomAD3 exomes AF: 0.0000963 AC: 24AN: 249116Hom.: 3 AF XY: 0.0000743 AC XY: 10AN XY: 134646
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1457944Hom.: 2 Cov.: 44 AF XY: 0.0000110 AC XY: 8AN XY: 725228
GnomAD4 genome ? AF: 0.0000330 AC: 5AN: 151576Hom.: 1 Cov.: 35 AF XY: 0.0000405 AC XY: 3AN XY: 74050
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.208G>T (p.A70S) alteration is located in exon 1 (coding exon 1) of the MRGPRX1 gene. This alteration results from a G to T substitution at nucleotide position 208, causing the alanine (A) at amino acid position 70 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