rs11100494

chr4-163349101-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006174.4(NPY5R):c.-9-1164C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0794 in 152,228 control chromosomes in the GnomAD database, including 541 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 0.079 (541 hom., cov: 32)
• Consequence: NPY5R NM_006174.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

Genes affected

NPY5R (HGNC:7958): (neuropeptide Y receptor Y5) The protein encoded by this gene is a receptor for neuropeptide Y and peptide YY. The encoded protein appears to be involved in regulating food intake, with defects in this gene being associated with eating disorders. Also, the encoded protein is involved in a pathway that protects neuroblastoma cells from chemotherapy-induced cell death, providing a possible therapeutic target against neuroblastoma. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY5R	NM_006174.4	c.-9-1164C>A		intron_variant		ENST00000338566.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPY5R	ENST00000338566.8	c.-9-1164C>A		intron_variant		1	NM_006174.4	P1
NPY5R	ENST00000515560.1	c.-9-1164C>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12100 AN: 152110 Hom.: 545 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0952

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0752

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

GnomAD4 genome AF: 0.0794 AC: 12093 AN: 152228 Hom.: 541 Cov.: 32 AF XY: 0.0813 AC XY: 6051 AN XY: 74434

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.0954

Gnomad4 ASJ AF: 0.0662

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.0668

Gnomad4 OTH AF: 0.0744

Alfa AF: 0.0708 Hom.: 531

Bravo AF: 0.0819

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.7
Dann	Benign	0.73

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: rs11100494; hg19: chr4-164270253;