NM_002447.4:c.4129C>T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002447.4(MST1R):c.4129C>T(p.Gln1377*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,614,130 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 (no stars).
Frequency
Consequence
NM_002447.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251462Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135900
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461886Hom.: 0 Cov.: 30 AF XY: 0.0000660 AC XY: 48AN XY: 727242
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Submissions by phenotype
not provided Uncertain:1
The MST1R p.Gln1271* variant was not identified in the literature nor was it identified in the ClinVar or Cosmic databases but was identified in dbSNP (ID: rs368400291) and LOVD 3.0. The variant was identified in control databases in 6 of 282850 chromosomes at a frequency of 0.000021 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 5 of 129156 chromosomes (freq: 0.000039) and South Asian in 1 of 30616 chromosomes (freq: 0.000033), but was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), and Other populations. The c.3811C>T variant leads to a premature stop codon at position 1271 which is predicted to lead to a truncated or absent protein. Loss of function variants of the MST1R gene are not an established mechanism of disease, therefore the impact of this variant on the protein is not known. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at