4-163335583-A-G

Variant names:

• chr4-163335583-A-G
• rs6837793
• ENST00000967840.1:c.-151-8878T>C

Variant summary

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

The ENST00000511901.1(NPY1R):​c.-152+8722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,118 control chromosomes in the GnomAD database, including 55,506 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 (55506 hom., cov: 31)
• Consequence: NPY1R ENST00000511901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 8 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=-0.95).
• 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: ENST00000511901.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY1R	ENST00000967840.1		c.-151-8878T>C		intron	N/A	ENSP00000637899.1
	NPY1R	ENST00000511901.1	TSL:3	c.-152+8722T>C		intron	N/A	ENSP00000423878.1	D6RC44

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129144 AN: 152000 Hom.: 55498 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.849 AC: 129191 AN: 152118 Hom.: 55506 Cov.: 31 AF XY: 0.853 AC XY: 63426 AN XY: 74358

African (AFR) AF: 0.699 AC: 28991 AN: 41460

American (AMR) AF: 0.900 AC: 13759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3059 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5137 AN: 5174

South Asian (SAS) AF: 0.911 AC: 4398 AN: 4828

European-Finnish (FIN) AF: 0.919 AC: 9735 AN: 10590

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61230 AN: 67994

Other (OTH) AF: 0.843 AC: 1779 AN: 2110

Alfa AF: 0.873 Hom.: 9852

Bravo AF: 0.842

Asia WGS AF: 0.903 AC: 3140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.31
PhyloP100		-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6837793;

hg19: chr4-164256735;