chr3-49887468-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002447.4(MST1R):c.4042C>A(p.Leu1348Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,614,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002447.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MST1R | NM_002447.4 | c.4042C>A | p.Leu1348Met | missense_variant | 20/20 | ENST00000296474.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MST1R | ENST00000296474.8 | c.4042C>A | p.Leu1348Met | missense_variant | 20/20 | 1 | NM_002447.4 | P2 | |
MST1R | ENST00000621387.4 | c.3724C>A | p.Leu1242Met | missense_variant | 18/18 | 1 | |||
MST1R | ENST00000344206.8 | c.3895C>A | p.Leu1299Met | missense_variant | 19/19 | 5 | A2 | ||
MST1R | ENST00000411578.6 | c.*864C>A | 3_prime_UTR_variant, NMD_transcript_variant | 19/19 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251446Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135916
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461876Hom.: 0 Cov.: 30 AF XY: 0.0000399 AC XY: 29AN XY: 727242
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.4042C>A (p.L1348M) alteration is located in exon 20 (coding exon 20) of the MST1R gene. This alteration results from a C to A substitution at nucleotide position 4042, causing the leucine (L) at amino acid position 1348 to be replaced by a methionine (M). 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