rs12507653

Variant names:

• chr4-163333181-T-A
• rs12507653
• ENST00000967840.1:c.-151-6476A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-163333181-T-A
• chr4-163333181-T-G

Variant summary

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

The ENST00000511901.1(NPY1R):​c.-151-6476A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,746 control chromosomes in the GnomAD database, including 25,066 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 0.55 (25066 hom., cov: 30)
• Consequence: NPY1R ENST00000511901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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.-151-6476A>T		intron	N/A	ENSP00000637899.1
	NPY1R	ENST00000511901.1	TSL:3	c.-151-6476A>T		intron	N/A	ENSP00000423878.1	D6RC44
	NPY1R	ENST00000504790.1	TSL:2	c.-537A>T		upstream_gene	N/A	ENSP00000427564.1	D6RI97

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83070 AN: 151628 Hom.: 25070 Cov.: 30

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.547 AC: 83069 AN: 151746 Hom.: 25066 Cov.: 30 AF XY: 0.547 AC XY: 40566 AN XY: 74180

African (AFR) AF: 0.277 AC: 11465 AN: 41368

American (AMR) AF: 0.653 AC: 9948 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2105 AN: 3472

East Asian (EAS) AF: 0.590 AC: 3033 AN: 5140

South Asian (SAS) AF: 0.622 AC: 2962 AN: 4764

European-Finnish (FIN) AF: 0.554 AC: 5846 AN: 10548

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45689 AN: 67914

Other (OTH) AF: 0.564 AC: 1186 AN: 2102

Alfa AF: 0.471 Hom.: 1430

Bravo AF: 0.547

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.60
PhyloP100		-0.74
PromoterAI		-0.0021	Neutral

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: rs12507653;

hg19: chr4-164254333;