rs533872004
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002447.4(MST1R):c.4171C>T(p.Arg1391Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,614,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 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
Publications
- nasopharyngeal carcinoma, susceptibility to, 3Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152272Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000278 AC: 7AN: 251394 AF XY: 0.0000368 show subpopulations
GnomAD4 exome AF: 0.0000451 AC: 66AN: 1461864Hom.: 0 Cov.: 30 AF XY: 0.0000426 AC XY: 31AN XY: 727232 show subpopulations
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74398 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4171C>T (p.R1391W) alteration is located in exon 20 (coding exon 20) of the MST1R gene. This alteration results from a C to T substitution at nucleotide position 4171, causing the arginine (R) at amino acid position 1391 to be replaced by a tryptophan (W). 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