NM_000909.6:c.*792T>C

Variant names:

• chr4-163324511-A-G
• rs4552421
• NM_000909.6:c.*792T>C

Variant summary

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

The NM_000909.6(NPY1R):​c.*792T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,064 control chromosomes in the GnomAD database, including 55,404 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 0.85 (55403 hom., cov: 31)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: NPY1R NM_000909.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606
• Publications: 4 publications found

Genes affected

NPY1R (HGNC:7956): (neuropeptide Y receptor Y1) This gene belongs to the G-protein-coupled receptor superfamily. The encoded transmembrane protein mediates the function of neuropeptide Y (NPY), a neurotransmitter, and peptide YY (PYY), a gastrointestinal hormone. The encoded receptor undergoes fast agonist-induced internalization through clathrin-coated pits and is subsequently recycled back to the cell membrane. Activation of Y1 receptors may result in mobilization of intracellular calcium and inhibition of adenylate cyclase activity. [provided by RefSeq, Aug 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000909.6. 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
	NPY1R	NM_000909.6	MANE Select	c.*792T>C		3_prime_UTR	Exon 3 of 3	NP_000900.1	P25929

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY1R	ENST00000296533.3	TSL:1 MANE Select	c.*792T>C		3_prime_UTR	Exon 3 of 3	ENSP00000354652.2	P25929
	NPY1R	ENST00000875543.1		c.*792T>C		3_prime_UTR	Exon 3 of 3	ENSP00000545602.1
	NPY1R	ENST00000875544.1		c.*792T>C		3_prime_UTR	Exon 3 of 3	ENSP00000545603.1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128850 AN: 151942 Hom.: 55397 Cov.: 31

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.852

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.848 AC: 128904 AN: 152060 Hom.: 55403 Cov.: 31 AF XY: 0.852 AC XY: 63281 AN XY: 74308

African (AFR) AF: 0.694 AC: 28730 AN: 41426

American (AMR) AF: 0.894 AC: 13665 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3060 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5138 AN: 5176

South Asian (SAS) AF: 0.912 AC: 4393 AN: 4816

European-Finnish (FIN) AF: 0.917 AC: 9718 AN: 10592

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61315 AN: 67972

Other (OTH) AF: 0.844 AC: 1783 AN: 2112

Alfa AF: 0.876 Hom.: 17981

Bravo AF: 0.840

Asia WGS AF: 0.892 AC: 3099 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.82
PhyloP100		0.61
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: rs4552421; hg19: chr4-164245663;