chr4-72040119-G-T

Variant names:

• chr4-72040119-G-T
• rs13150414
• NM_004885.3:c.-8+7919G>T

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+7919G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,568 control chromosomes in the GnomAD database, including 9,587 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 0.35 (9587 hom., cov: 33)
• Consequence: NPFFR2 NM_004885.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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+7919G>T		intron	N/A	NP_004876.3	Q9Y5X5-2
	NPFFR2	NM_001144756.2		c.-110+706G>T		intron	N/A	NP_001138228.1	Q9Y5X5-3
	NPFFR2	NM_053036.3		c.-8+706G>T		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+7919G>T		intron	N/A	ENSP00000307822.7	Q9Y5X5-2
	NPFFR2	ENST00000395999.5	TSL:1	c.-110+706G>T		intron	N/A	ENSP00000379321.1	Q9Y5X5-3
	NPFFR2	ENST00000358749.3	TSL:1	c.-8+706G>T		intron	N/A	ENSP00000351599.3	Q9Y5X5-2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52740 AN: 151450 Hom.: 9573 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.348 AC: 52789 AN: 151568 Hom.: 9587 Cov.: 33 AF XY: 0.349 AC XY: 25838 AN XY: 74014

African (AFR) AF: 0.321 AC: 13280 AN: 41312

American (AMR) AF: 0.393 AC: 5980 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3466

East Asian (EAS) AF: 0.678 AC: 3494 AN: 5150

South Asian (SAS) AF: 0.463 AC: 2225 AN: 4806

European-Finnish (FIN) AF: 0.289 AC: 3027 AN: 10470

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22038 AN: 67828

Other (OTH) AF: 0.380 AC: 799 AN: 2100

Alfa AF: 0.202 Hom.: 435

Bravo AF: 0.354

Asia WGS AF: 0.555 AC: 1909 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.13
PhyloP100		0.34
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: rs13150414; hg19: chr4-72905836;