NM_004885.3:c.-8+15240G>C

Variant names:

• chr4-72047440-G-C
• rs9637554
• NM_004885.3:c.-8+15240G>C

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+15240G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,072 control chromosomes in the GnomAD database, including 61,355 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 0.89 (61355 hom., cov: 31)
• Consequence: NPFFR2 NM_004885.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPFFR2	NM_004885.3	c.-8+15240G>C		intron_variant	Intron 1 of 3	ENST00000308744.12	NP_004876.3
NPFFR2	NM_001144756.2	c.-110+8027G>C		intron_variant	Intron 1 of 4		NP_001138228.1
NPFFR2	NM_053036.3	c.-8+8027G>C		intron_variant	Intron 1 of 3		NP_444264.1
NPFFR2	XM_011531554.3	c.304+8027G>C		intron_variant	Intron 1 of 2		XP_011529856.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPFFR2	ENST00000308744.12	c.-8+15240G>C		intron_variant	Intron 1 of 3	1	NM_004885.3	ENSP00000307822.7
NPFFR2	ENST00000395999.5	c.-110+8027G>C		intron_variant	Intron 1 of 4	1		ENSP00000379321.1
NPFFR2	ENST00000358749.3	c.-8+8027G>C		intron_variant	Intron 1 of 3	1		ENSP00000351599.3
NPFFR2	ENST00000344413.6	c.-21+15240G>C		intron_variant	Intron 1 of 2	1		ENSP00000340789.6

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135236 AN: 151954 Hom.: 61323 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.890 AC: 135323 AN: 152072 Hom.: 61355 Cov.: 31 AF XY: 0.890 AC XY: 66117 AN XY: 74328

African (AFR) AF: 0.750 AC: 31091 AN: 41448

American (AMR) AF: 0.900 AC: 13736 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3284 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2682 AN: 5124

South Asian (SAS) AF: 0.874 AC: 4214 AN: 4824

European-Finnish (FIN) AF: 0.980 AC: 10403 AN: 10618

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66846 AN: 68004

Other (OTH) AF: 0.893 AC: 1884 AN: 2110

Alfa AF: 0.934 Hom.: 8305

Bravo AF: 0.874

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.20
PhyloP100		-0.21
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: rs9637554; hg19: chr4-72913157;