rs892757171
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017761.4(PNRC2):c.254T>C(p.Phe85Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017761.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNRC2 | ENST00000334351.8 | c.254T>C | p.Phe85Ser | missense_variant | Exon 3 of 3 | 1 | NM_017761.4 | ENSP00000334840.7 | ||
PNRC2 | ENST00000374468.1 | c.254T>C | p.Phe85Ser | missense_variant | Exon 3 of 3 | 2 | ENSP00000363592.1 | |||
PNRC2 | ENST00000647887.1 | c.254T>C | p.Phe85Ser | missense_variant | Exon 4 of 4 | ENSP00000497590.1 | ||||
PNRC2 | ENST00000471915.5 | c.*246T>C | downstream_gene_variant | 3 | ENSP00000464216.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000234 AC: 1AN: 42718Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 21450
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461666Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727140
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.254T>C (p.F85S) alteration is located in exon 3 (coding exon 1) of the PNRC2 gene. This alteration results from a T to C substitution at nucleotide position 254, causing the phenylalanine (F) at amino acid position 85 to be replaced by a serine (S). 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