chr15-75207166-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015492.5(C15orf39):c.1118C>T(p.Pro373Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,936 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015492.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C15orf39 | NM_015492.5 | c.1118C>T | p.Pro373Leu | missense_variant | Exon 2 of 3 | ENST00000394987.5 | NP_056307.3 | |
C15orf39 | XM_047432864.1 | c.1118C>T | p.Pro373Leu | missense_variant | Exon 3 of 4 | XP_047288820.1 | ||
C15orf39 | XM_047432865.1 | c.284C>T | p.Pro95Leu | missense_variant | Exon 4 of 5 | XP_047288821.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C15orf39 | ENST00000394987.5 | c.1118C>T | p.Pro373Leu | missense_variant | Exon 2 of 3 | 1 | NM_015492.5 | ENSP00000378438.4 | ||
C15orf39 | ENST00000567617.1 | c.1118C>T | p.Pro373Leu | missense_variant | Exon 1 of 2 | 1 | ENSP00000458025.1 | |||
C15orf39 | ENST00000360639.6 | c.1118C>T | p.Pro373Leu | missense_variant | Exon 2 of 3 | 2 | ENSP00000353854.2 | |||
C15orf39 | ENST00000565074.1 | c.722C>T | p.Pro241Leu | missense_variant | Exon 1 of 1 | 6 | ENSP00000454405.1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152114Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251360Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135866
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461704Hom.: 1 Cov.: 70 AF XY: 0.00000963 AC XY: 7AN XY: 727174
GnomAD4 genome AF: 0.000177 AC: 27AN: 152232Hom.: 0 Cov.: 29 AF XY: 0.000202 AC XY: 15AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1118C>T (p.P373L) alteration is located in exon 2 (coding exon 1) of the C15orf39 gene. This alteration results from a C to T substitution at nucleotide position 1118, causing the proline (P) at amino acid position 373 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