11-118117314-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_019894.4(TMPRSS4):c.1162G>C(p.Gly388Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000465 in 1,614,116 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G388C) has been classified as Uncertain significance.
Frequency
Consequence
NM_019894.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMPRSS4 | NM_019894.4 | c.1162G>C | p.Gly388Arg | missense_variant | 12/13 | ENST00000437212.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMPRSS4 | ENST00000437212.8 | c.1162G>C | p.Gly388Arg | missense_variant | 12/13 | 1 | NM_019894.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251208Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135758
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461832Hom.: 0 Cov.: 30 AF XY: 0.0000426 AC XY: 31AN XY: 727218
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2021 | The c.1162G>C (p.G388R) alteration is located in exon 12 (coding exon 12) of the TMPRSS4 gene. This alteration results from a G to C substitution at nucleotide position 1162, causing the glycine (G) at amino acid position 388 to be replaced by an arginine (R). 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