rs12512687

Variant names:

• chr4-163352044-G-A
• rs12512687
• XM_005263038.4:c.*433G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-163352044-G-A
• chr4-163352044-G-T

Variant summary

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

The XM_005263038.4(NPY5R):​c.*433G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 156,200 control chromosomes in the GnomAD database, including 553 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 (539 hom., cov: 33)
  • Exomes 𝑓: 0.084 (14 hom.)
• Consequence: NPY5R XM_005263038.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 1 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=-0.9).
• 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 rank	MANE	Protein	UniProt
NPY5R	NM_006174.4	c.*433G>A		downstream_gene_variant		ENST00000338566.8	NP_006165.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY5R	ENST00000338566.8	c.*433G>A		downstream_gene_variant		1	NM_006174.4	ENSP00000339377.3
NPY5R	ENST00000515560.1	c.*433G>A		downstream_gene_variant		2		ENSP00000423917.1

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12082 AN: 151930 Hom.: 543 Cov.: 33

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.0664

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: 0.0755

GnomAD4 exome AF: 0.0838 AC: 348 AN: 4152 Hom.: 14 AF XY: 0.0817 AC XY: 175 AN XY: 2142

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.100 AC: 2 AN: 20

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 1 AN: 16

East Asian (EAS) AF: 0.0625 AC: 1 AN: 16

South Asian (SAS) AF: 0.286 AC: 4 AN: 14

European-Finnish (FIN) AF: 0.0881 AC: 324 AN: 3676

Middle Eastern (MID) AF: 0.250 AC: 1 AN: 4

European-Non Finnish (NFE) AF: 0.0357 AC: 13 AN: 364

Other (OTH) AF: 0.0500 AC: 2 AN: 40

GnomAD4 genome AF: 0.0794 AC: 12075 AN: 152048 Hom.: 539 Cov.: 33 AF XY: 0.0814 AC XY: 6046 AN XY: 74320

African (AFR) AF: 0.0772 AC: 3204 AN: 41508

American (AMR) AF: 0.0948 AC: 1448 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0664 AC: 230 AN: 3466

East Asian (EAS) AF: 0.141 AC: 729 AN: 5182

South Asian (SAS) AF: 0.177 AC: 852 AN: 4816

European-Finnish (FIN) AF: 0.0821 AC: 866 AN: 10544

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

European-Non Finnish (NFE) AF: 0.0669 AC: 4543 AN: 67942

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

Alfa AF: 0.0358 Hom.: 30

Bravo AF: 0.0817

Asia WGS AF: 0.148 AC: 513 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12512687; hg19: chr4-164273196;