chr3-49890546-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_002447.4(MST1R):c.3749C>T(p.Pro1250Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002447.4 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 |
---|---|---|---|---|---|---|---|
MST1R | NM_002447.4 | c.3749C>T | p.Pro1250Leu | missense_variant | 18/20 | ENST00000296474.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MST1R | ENST00000296474.8 | c.3749C>T | p.Pro1250Leu | missense_variant | 18/20 | 1 | NM_002447.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251284Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135834
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727228
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.3749C>T (p.P1250L) alteration is located in exon 18 (coding exon 18) of the MST1R gene. This alteration results from a C to T substitution at nucleotide position 3749, causing the proline (P) at amino acid position 1250 to be replaced by a leucine (L). 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