rs17695224

Variant names:

• chr19-51820963-G-A
• rs17695224
• NM_002030.5:c.-10-2776G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-51820963-G-A
• chr19-51820963-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002030.5(FPR3):​c.-10-2776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,162 control chromosomes in the GnomAD database, including 4,416 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 0.23 (4416 hom., cov: 32)
• Consequence: FPR3 NM_002030.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 58 publications found

Genes affected

FPR3 (HGNC:3828): (formyl peptide receptor 3) Predicted to enable N-formyl peptide receptor activity and complement receptor activity. Predicted to be involved in several processes, including complement receptor mediated signaling pathway; phospholipase C-activating G protein-coupled receptor signaling pathway; and positive regulation of cytosolic calcium ion concentration. Predicted to act upstream of or within G protein-coupled receptor signaling pathway. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ZNF577 (HGNC:28673): (zinc finger protein 577) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002030.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FPR3	NM_002030.5	MANE Select	c.-10-2776G>A		intron	N/A	NP_002021.3
	ZNF577	NR_163433.1		n.2153-6986C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FPR3	ENST00000339223.5	TSL:1 MANE Select	c.-10-2776G>A		intron	N/A	ENSP00000341821.3
	FPR3	ENST00000595991.1	TSL:4	c.-10-2776G>A		intron	N/A	ENSP00000470471.1
	ZNF577	ENST00000638827.1	TSL:5	n.*600-9289C>T		intron	N/A	ENSP00000492704.1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35313 AN: 152044 Hom.: 4417 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.232 AC: 35318 AN: 152162 Hom.: 4416 Cov.: 32 AF XY: 0.231 AC XY: 17189 AN XY: 74388

African (AFR) AF: 0.148 AC: 6163 AN: 41512

American (AMR) AF: 0.318 AC: 4866 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1103 AN: 5182

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1905 AN: 10606

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18125 AN: 67978

Other (OTH) AF: 0.266 AC: 563 AN: 2114

Alfa AF: 0.259 Hom.: 24790

Bravo AF: 0.239

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17695224; hg19: chr19-52324216;