rs6446809

Positions:

• chr4-72059777-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_004885.3(NPFFR2):​c.-8+27577T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00588 in 152,188 control chromosomes in the GnomAD database, including 8 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 0.0059 (8 hom., cov: 32)
• Consequence: NPFFR2 NM_004885.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPFFR2	NM_004885.3	c.-8+27577T>G		intron_variant		ENST00000308744.12	NP_004876.3
NPFFR2	NM_001144756.2	c.-109-9136T>G		intron_variant			NP_001138228.1
NPFFR2	NM_053036.3	c.-8+20364T>G		intron_variant			NP_444264.1
NPFFR2	XM_011531554.3	c.304+20364T>G		intron_variant			XP_011529856.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPFFR2	ENST00000308744.12	c.-8+27577T>G		intron_variant		1	NM_004885.3	ENSP00000307822.7
NPFFR2	ENST00000395999.5	c.-109-9136T>G		intron_variant		1		ENSP00000379321.1
NPFFR2	ENST00000358749.3	c.-8+20364T>G		intron_variant		1		ENSP00000351599.3
NPFFR2	ENST00000344413.6	c.-21+27577T>G		intron_variant		1		ENSP00000340789.6

Frequencies

GnomAD3 genomes AF: 0.00586 AC: 891 AN: 152070 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00970

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0108

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.000659

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00144

Gnomad OTH AF: 0.0106

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

GnomAD4 genome AF: 0.00588 AC: 895 AN: 152188 Hom.: 8 Cov.: 32 AF XY: 0.00567 AC XY: 422 AN XY: 74420

Gnomad4 AFR AF: 0.00977

Gnomad4 AMR AF: 0.0108

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.000659

Gnomad4 NFE AF: 0.00144

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.00469 Hom.: 1

Bravo AF: 0.00711

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs6446809; hg19: chr4-72925494;