10-70255653-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_022146.5(NPFFR1):c.597G>A(p.Pro199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000333 in 1,593,622 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000033 ( 1 hom. )
Consequence
NPFFR1
NM_022146.5 synonymous
NM_022146.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.43
Genes affected
NPFFR1 (HGNC:17425): (neuropeptide FF receptor 1) Predicted to enable G protein-coupled receptor activity and peptide binding activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Located in cilium. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP7
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Synonymous conserved (PhyloP=-1.43 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPFFR1 | NM_022146.5 | c.597G>A | p.Pro199= | synonymous_variant | 4/4 | ENST00000277942.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPFFR1 | ENST00000277942.7 | c.597G>A | p.Pro199= | synonymous_variant | 4/4 | 5 | NM_022146.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152046Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000377 AC: 8AN: 212232Hom.: 0 AF XY: 0.0000694 AC XY: 8AN XY: 115274
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GnomAD4 exome AF: 0.0000333 AC: 48AN: 1441576Hom.: 1 Cov.: 52 AF XY: 0.0000420 AC XY: 30AN XY: 714980
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at