rs7679840
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004885.3(NPFFR2):c.328+3273C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,456 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 ( 0 hom., cov: 31)
Consequence
NPFFR2
NM_004885.3 intron
NM_004885.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.89
Genes affected
NPFFR2 (HGNC:4525): (neuropeptide FF receptor 2) This gene encodes a member of a subfamily of G-protein-coupled neuropeptide receptors. This protein is activated by the neuropeptides A-18-amide (NPAF) and F-8-amide (NPFF) and may function in pain modulation and regulation of the opioid system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPFFR2 | NM_004885.3 | c.328+3273C>A | intron_variant | ENST00000308744.12 | |||
NPFFR2 | NM_001144756.2 | c.337+3273C>A | intron_variant | ||||
NPFFR2 | NM_053036.3 | c.328+3273C>A | intron_variant | ||||
NPFFR2 | XM_011531554.3 | c.305-5848C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPFFR2 | ENST00000308744.12 | c.328+3273C>A | intron_variant | 1 | NM_004885.3 | P4 | |||
NPFFR2 | ENST00000344413.6 | c.-20-5848C>A | intron_variant | 1 | |||||
NPFFR2 | ENST00000358749.3 | c.328+3273C>A | intron_variant | 1 | P4 | ||||
NPFFR2 | ENST00000395999.5 | c.337+3273C>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151456Hom.: 0 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151456Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73958
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ClinVar
Not reported inComputational scores
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Name
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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