chr16-563683-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145270.3(PRR35):c.389C>T(p.Pro130Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000153 in 1,565,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145270.3 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 |
---|---|---|---|---|---|---|---|---|
PRR35 | NM_145270.3 | c.389C>T | p.Pro130Leu | missense_variant | Exon 2 of 3 | ENST00000409413.4 | NP_660313.1 | |
PRR35 | XM_017022959.3 | c.389C>T | p.Pro130Leu | missense_variant | Exon 2 of 3 | XP_016878448.1 | ||
PRR35 | XM_017022960.3 | c.389C>T | p.Pro130Leu | missense_variant | Exon 3 of 4 | XP_016878449.1 | ||
PRR35 | XM_017022961.1 | c.170+219C>T | intron_variant | Intron 2 of 3 | XP_016878450.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000238 AC: 4AN: 167886Hom.: 0 AF XY: 0.0000431 AC XY: 4AN XY: 92776
GnomAD4 exome AF: 0.0000163 AC: 23AN: 1413334Hom.: 0 Cov.: 33 AF XY: 0.0000243 AC XY: 17AN XY: 700170
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.389C>T (p.P130L) alteration is located in exon 2 (coding exon 1) of the PRR35 gene. This alteration results from a C to T substitution at nucleotide position 389, causing the proline (P) at amino acid position 130 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