rs4475104

Variant names:

• chr4-163342134-C-G
• rs4475104
• ENST00000967840.1:c.-152+2640G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-163342134-C-G
• chr4-163342134-C-T

Variant summary

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

The ENST00000511901.1(NPY1R):​c.-152+2171G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,990 control chromosomes in the GnomAD database, including 3,441 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 0.19 (3441 hom., cov: 33)
• Consequence: NPY1R ENST00000511901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 1 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 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.-152+2640G>C		intron	N/A	ENSP00000637899.1
	NPY1R	ENST00000511901.1	TSL:3	c.-152+2171G>C		intron	N/A	ENSP00000423878.1	D6RC44

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28427 AN: 151872 Hom.: 3430 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.187 AC: 28477 AN: 151990 Hom.: 3441 Cov.: 33 AF XY: 0.189 AC XY: 14070 AN XY: 74294

African (AFR) AF: 0.321 AC: 13285 AN: 41428

American (AMR) AF: 0.197 AC: 3001 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3466

East Asian (EAS) AF: 0.317 AC: 1643 AN: 5176

South Asian (SAS) AF: 0.231 AC: 1110 AN: 4814

European-Finnish (FIN) AF: 0.131 AC: 1384 AN: 10554

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7018 AN: 67974

Other (OTH) AF: 0.163 AC: 345 AN: 2112

Alfa AF: 0.0729 Hom.: 91

Bravo AF: 0.198

Asia WGS AF: 0.236 AC: 821 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.4
DANN	Benign	0.74
PhyloP100		-0.49

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: rs4475104;

hg19: chr4-164263286;