12-53507136-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003717.4(NPFF):c.109G>C(p.Asp37His) variant causes a missense change. The variant allele was found at a frequency of 0.0000254 in 1,613,730 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPFF | ENST00000267017.4 | c.109G>C | p.Asp37His | missense_variant | Exon 2 of 3 | 1 | NM_003717.4 | ENSP00000267017.3 | ||
ATF7-NPFF | ENST00000591834.1 | c.1241G>C | p.Arg414Thr | missense_variant | Exon 12 of 13 | 5 | ENSP00000466174.1 | |||
NPFF | ENST00000448979.4 | n.349G>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250660Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135466
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461560Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727078
GnomAD4 genome AF: 0.000151 AC: 23AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.109G>C (p.D37H) alteration is located in exon 2 (coding exon 2) of the NPFF gene. This alteration results from a G to C substitution at nucleotide position 109, causing the aspartic acid (D) at amino acid position 37 to be replaced by a histidine (H). 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