16-715345-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024042.4(METRN):c.56C>T(p.Pro19Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024042.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
METRN | ENST00000568223.7 | c.56C>T | p.Pro19Leu | missense_variant | Exon 1 of 4 | 1 | NM_024042.4 | ENSP00000455068.1 | ||
METRN | ENST00000219542.3 | c.8C>T | p.Pro3Leu | missense_variant | Exon 1 of 3 | 2 | ENSP00000219542.3 | |||
METRN | ENST00000570132.1 | n.56C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 3 | ENSP00000456647.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1189388Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 579152
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.56C>T (p.P19L) alteration is located in exon 1 (coding exon 1) of the METRN gene. This alteration results from a C to T substitution at nucleotide position 56, causing the proline (P) at amino acid position 19 to be replaced by a leucine (L). 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