chr10-70255521-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_022146.5(NPFFR1):c.729C>G(p.Leu243=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,548,672 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0047 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00061 ( 1 hom. )
Consequence
NPFFR1
NM_022146.5 synonymous
NM_022146.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0260
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 Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 10-70255521-G-C is Benign according to our data. Variant chr10-70255521-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 708807.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.026 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000613 (856/1396384) while in subpopulation AFR AF= 0.0164 (517/31506). AF 95% confidence interval is 0.0152. There are 1 homozygotes in gnomad4_exome. There are 361 alleles in male gnomad4_exome subpopulation. Median coverage is 40. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPFFR1 | NM_022146.5 | c.729C>G | p.Leu243= | synonymous_variant | 4/4 | ENST00000277942.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPFFR1 | ENST00000277942.7 | c.729C>G | p.Leu243= | synonymous_variant | 4/4 | 5 | NM_022146.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00473 AC: 720AN: 152170Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00113 AC: 168AN: 148862Hom.: 0 AF XY: 0.000965 AC XY: 77AN XY: 79784
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GnomAD4 exome AF: 0.000613 AC: 856AN: 1396384Hom.: 1 Cov.: 40 AF XY: 0.000524 AC XY: 361AN XY: 688364
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GnomAD4 genome ? AF: 0.00473 AC: 721AN: 152288Hom.: 4 Cov.: 32 AF XY: 0.00439 AC XY: 327AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 30, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at