chr12-53506843-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003717.4(NPFF):āc.275G>Cā(p.Arg92Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,452,180 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R92Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_003717.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPFF | ENST00000267017.4 | c.275G>C | p.Arg92Pro | missense_variant | Exon 3 of 3 | 1 | NM_003717.4 | ENSP00000267017.3 | ||
ATF7-NPFF | ENST00000591834 | c.*15G>C | 3_prime_UTR_variant | Exon 13 of 13 | 5 | ENSP00000466174.1 | ||||
NPFF | ENST00000448979.4 | n.515G>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1452180Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 721704
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.