rs17849971
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002029.4(FPR1):c.993C>T(p.Thr331=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0273 in 1,614,118 control chromosomes in the GnomAD database, including 776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.020 ( 49 hom., cov: 32)
Exomes 𝑓: 0.028 ( 727 hom. )
Consequence
FPR1
NM_002029.4 synonymous
NM_002029.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.327
Genes affected
FPR1 (HGNC:3826): (formyl peptide receptor 1) This gene encodes a G protein-coupled receptor of mammalian phagocytic cells that is a member of the G-protein coupled receptor 1 family. The protein mediates the response of phagocytic cells to invasion of the host by microorganisms and is important in host defense and inflammation.[provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 19-51746002-G-A is Benign according to our data. Variant chr19-51746002-G-A is described in ClinVar as [Benign]. Clinvar id is 402875.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.327 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0204 (3102/152246) while in subpopulation NFE AF= 0.0318 (2163/68008). AF 95% confidence interval is 0.0307. There are 49 homozygotes in gnomad4. There are 1515 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 49 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPR1 | NM_002029.4 | c.993C>T | p.Thr331= | synonymous_variant | 2/2 | ENST00000304748.5 | |
FPR1 | NM_001193306.2 | c.993C>T | p.Thr331= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPR1 | ENST00000304748.5 | c.993C>T | p.Thr331= | synonymous_variant | 2/2 | 1 | NM_002029.4 | P1 | |
FPR1 | ENST00000594900.2 | c.993C>T | p.Thr331= | synonymous_variant | 3/3 | 4 | P1 | ||
FPR1 | ENST00000595042.5 | c.993C>T | p.Thr331= | synonymous_variant | 3/3 | 2 | P1 | ||
FPR1 | ENST00000600815.2 | c.993C>T | p.Thr331= | synonymous_variant | 2/2 | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0204 AC: 3101AN: 152128Hom.: 49 Cov.: 32
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GnomAD3 exomes AF: 0.0210 AC: 5283AN: 251282Hom.: 89 AF XY: 0.0211 AC XY: 2870AN XY: 135808
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GnomAD4 exome AF: 0.0280 AC: 40904AN: 1461872Hom.: 727 Cov.: 71 AF XY: 0.0276 AC XY: 20096AN XY: 727232
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GnomAD4 genome ? AF: 0.0204 AC: 3102AN: 152246Hom.: 49 Cov.: 32 AF XY: 0.0203 AC XY: 1515AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Gingival disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational 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