chr10-70255434-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_022146.5(NPFFR1):c.816G>A(p.Leu272=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 1,547,580 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 52 hom. )
Consequence
NPFFR1
NM_022146.5 synonymous
NM_022146.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.800
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=-0.54).
BP6
Variant 10-70255434-C-T is Benign according to our data. Variant chr10-70255434-C-T is described in ClinVar as [Benign]. Clinvar id is 769781.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.8 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00288 (438/152282) while in subpopulation AMR AF= 0.025 (383/15306). AF 95% confidence interval is 0.023. There are 6 homozygotes in gnomad4. There are 238 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPFFR1 | NM_022146.5 | c.816G>A | p.Leu272= | synonymous_variant | 4/4 | ENST00000277942.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPFFR1 | ENST00000277942.7 | c.816G>A | p.Leu272= | synonymous_variant | 4/4 | 5 | NM_022146.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00286 AC: 435AN: 152164Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00959 AC: 1396AN: 145614Hom.: 49 AF XY: 0.00744 AC XY: 583AN XY: 78340
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GnomAD4 exome AF: 0.00137 AC: 1910AN: 1395298Hom.: 52 Cov.: 40 AF XY: 0.00118 AC XY: 812AN XY: 688408
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GnomAD4 genome AF: 0.00288 AC: 438AN: 152282Hom.: 6 Cov.: 32 AF XY: 0.00320 AC XY: 238AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2018 | - - |
Computational scores
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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