17-35764449-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145272.4(C17orf50):c.356C>T(p.Pro119Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,553,576 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145272.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C17orf50 | NM_145272.4 | c.356C>T | p.Pro119Leu | missense_variant | Exon 3 of 3 | ENST00000605587.2 | NP_660315.2 | |
MMP28 | XM_011525231.2 | c.1168+3303G>A | intron_variant | Intron 7 of 7 | XP_011523533.1 | |||
MMP28 | XM_017025064.2 | c.*27+3303G>A | intron_variant | Intron 7 of 7 | XP_016880553.1 | |||
MMP28 | NR_111988.2 | n.2100+1748G>A | intron_variant | Intron 8 of 8 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000701 AC: 11AN: 156976Hom.: 0 AF XY: 0.0000809 AC XY: 7AN XY: 86548
GnomAD4 exome AF: 0.0000235 AC: 33AN: 1401488Hom.: 0 Cov.: 31 AF XY: 0.0000245 AC XY: 17AN XY: 693062
GnomAD4 genome AF: 0.000276 AC: 42AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.000323 AC XY: 24AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.356C>T (p.P119L) alteration is located in exon 3 (coding exon 3) of the C17orf50 gene. This alteration results from a C to T substitution at nucleotide position 356, causing the proline (P) at amino acid position 119 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