rs11100494

Variant names:

• chr4-163349101-C-A
• rs11100494
• NM_006174.4:c.-9-1164C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006174.4. 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
	NPY5R	NM_006174.4	MANE Select	c.-9-1164C>A		intron	N/A	NP_006165.1	Q15761
	NPY5R	NM_001317091.2		c.-9-1164C>A		intron	N/A	NP_001304020.1	Q15761
	NPY5R	NM_001317092.2		c.-9-1164C>A		intron	N/A	NP_001304021.1	Q15761

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY5R	ENST00000338566.8	TSL:1 MANE Select	c.-9-1164C>A		intron	N/A	ENSP00000339377.3	Q15761
	NPY5R	ENST00000919920.1		c.-249C>A		5_prime_UTR	Exon 3 of 4	ENSP00000589979.1
	NPY5R	ENST00000515560.1	TSL:2	c.-9-1164C>A		intron	N/A	ENSP00000423917.1	Q15761

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

African (AFR) AF: 0.0772 AC: 3204 AN: 41512

American (AMR) AF: 0.0954 AC: 1459 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.141 AC: 730 AN: 5182

South Asian (SAS) AF: 0.177 AC: 852 AN: 4824

European-Finnish (FIN) AF: 0.0821 AC: 870 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0668 AC: 4546 AN: 68020

Other (OTH) AF: 0.0744 AC: 157 AN: 2110

Alfa AF: 0.0730 Hom.: 818

Bravo AF: 0.0819

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.73
PhyloP100		-0.56
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: rs11100494; hg19: chr4-164270253;