4-72053293-A-G

Variant names:

• chr4-72053293-A-G
• rs4694453
• NM_004885.3:c.-8+21093A>G

Variant summary

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

The NM_004885.3(NPFFR2):​c.-8+21093A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 151,630 control chromosomes in the GnomAD database, including 298 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 0.028 (298 hom., cov: 30)
• Consequence: NPFFR2 NM_004885.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 0 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004885.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPFFR2	NM_004885.3	MANE Select	c.-8+21093A>G		intron	N/A	NP_004876.3	Q9Y5X5-2
	NPFFR2	NM_001144756.2		c.-110+13880A>G		intron	N/A	NP_001138228.1	Q9Y5X5-3
	NPFFR2	NM_053036.3		c.-8+13880A>G		intron	N/A	NP_444264.1	Q9Y5X5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPFFR2	ENST00000308744.12	TSL:1 MANE Select	c.-8+21093A>G		intron	N/A	ENSP00000307822.7	Q9Y5X5-2
	NPFFR2	ENST00000395999.5	TSL:1	c.-110+13880A>G		intron	N/A	ENSP00000379321.1	Q9Y5X5-3
	NPFFR2	ENST00000358749.3	TSL:1	c.-8+13880A>G		intron	N/A	ENSP00000351599.3	Q9Y5X5-2

Frequencies

GnomAD3 genomes AF: 0.0280 AC: 4247 AN: 151512 Hom.: 298 Cov.: 30

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.000662

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00915

Gnomad OTH AF: 0.0336

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

GnomAD4 genome AF: 0.0281 AC: 4254 AN: 151630 Hom.: 298 Cov.: 30 AF XY: 0.0302 AC XY: 2238 AN XY: 74070

African (AFR) AF: 0.0186 AC: 768 AN: 41334

American (AMR) AF: 0.0363 AC: 551 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.0505 AC: 175 AN: 3464

East Asian (EAS) AF: 0.313 AC: 1598 AN: 5110

South Asian (SAS) AF: 0.0944 AC: 453 AN: 4800

European-Finnish (FIN) AF: 0.000662 AC: 7 AN: 10570

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00917 AC: 622 AN: 67856

Other (OTH) AF: 0.0328 AC: 69 AN: 2106

Alfa AF: 0.00130 Hom.: 2188

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-0.17
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: rs4694453; hg19: chr4-72919010;