chr11-118115223-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019894.4(TMPRSS4):c.1095A>T(p.Glu365Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,612,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019894.4 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 |
---|---|---|---|---|---|---|---|
TMPRSS4 | NM_019894.4 | c.1095A>T | p.Glu365Asp | missense_variant | 11/13 | ENST00000437212.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMPRSS4 | ENST00000437212.8 | c.1095A>T | p.Glu365Asp | missense_variant | 11/13 | 1 | NM_019894.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000323 AC: 8AN: 247718Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133406
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460662Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726332
GnomAD4 genome ? AF: 0.0000986 AC: 15AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2023 | The c.1095A>T (p.E365D) alteration is located in exon 11 (coding exon 11) of the TMPRSS4 gene. This alteration results from a A to T substitution at nucleotide position 1095, causing the glutamic acid (E) at amino acid position 365 to be replaced by an aspartic acid (D). 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