11-69005880-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_145015.5(MRGPRF):āc.430T>Cā(p.Ser144Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000354 in 1,411,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_145015.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRGPRF | NM_145015.5 | c.430T>C | p.Ser144Pro | missense_variant | 3/3 | ENST00000309099.7 | NP_659452.3 | |
MRGPRF | NM_001098515.2 | c.430T>C | p.Ser144Pro | missense_variant | 3/3 | NP_001091985.1 | ||
MRGPRF | XM_017017170.2 | c.430T>C | p.Ser144Pro | missense_variant | 3/3 | XP_016872659.1 | ||
MRGPRF | XM_024448339.2 | c.430T>C | p.Ser144Pro | missense_variant | 3/3 | XP_024304107.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000354 AC: 5AN: 1411966Hom.: 0 Cov.: 30 AF XY: 0.00000573 AC XY: 4AN XY: 697536
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.430T>C (p.S144P) alteration is located in exon 3 (coding exon 2) of the MRGPRF gene. This alteration results from a T to C substitution at nucleotide position 430, causing the serine (S) at amino acid position 144 to be replaced by a proline (P). 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
Publications
No publications associated with this variant yet.