12-53507423-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003717.4(NPFF):c.52G>A(p.Gly18Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003717.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPFF | NM_003717.4 | c.52G>A | p.Gly18Arg | missense_variant | 1/3 | ENST00000267017.4 | |
ATF7-NPFF | NR_159377.1 | n.1894-281G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPFF | ENST00000267017.4 | c.52G>A | p.Gly18Arg | missense_variant | 1/3 | 1 | NM_003717.4 | P1 | |
NPFF | ENST00000448979.4 | n.62G>A | non_coding_transcript_exon_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251084Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135726
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461728Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727164
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74440
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at