12-53507051-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003717.4(NPFF):c.194G>A(p.Arg65Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,870 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_003717.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
NPFF | ENST00000267017.4 | c.194G>A | p.Arg65Gln | missense_variant | Exon 2 of 3 | 1 | NM_003717.4 | ENSP00000267017.3 | ||
ATF7-NPFF | ENST00000591834.1 | c.1326G>A | p.Pro442Pro | synonymous_variant | Exon 12 of 13 | 5 | ENSP00000466174.1 | |||
NPFF | ENST00000448979.4 | n.434G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251258Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135792
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461784Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727208
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.194G>A (p.R65Q) alteration is located in exon 2 (coding exon 2) of the NPFF gene. This alteration results from a G to A substitution at nucleotide position 194, causing the arginine (R) at amino acid position 65 to be replaced by a glutamine (Q). 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