ENST00000511901.1:c.-152+2171G>C

Variant names:

• chr4-163342134-C-G
• rs4475104
• ENST00000511901.1:c.-152+2171G>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+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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY1R	XM_005263031.5	c.-152+2171G>C		intron_variant	Intron 1 of 2		XP_005263088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY1R	ENST00000511901.1	c.-152+2171G>C		intron_variant	Intron 1 of 1	3		ENSP00000423878.1

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 v4.3

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

Other links and lift over

dbSNP: rs4475104; hg19: chr4-164263286;