rs4057797

Variant names:

• chr4-163323901-T-A
• rs4057797
• NM_000909.6:c.*1402A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-163323901-T-A
• chr4-163323901-T-G

Variant summary

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

The NM_000909.6(NPY1R):​c.*1402A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,768 control chromosomes in the GnomAD database, including 20,824 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 0.50 (20824 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: NPY1R NM_000909.6 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY1R	NM_000909.6	c.*1402A>T		downstream_gene_variant		ENST00000296533.3	NP_000900.1
NPY1R	XM_005263031.5	c.*1402A>T		downstream_gene_variant			XP_005263088.1
NPY1R	XM_011532010.4	c.*1402A>T		downstream_gene_variant			XP_011530312.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY1R	ENST00000296533.3	c.*1402A>T		downstream_gene_variant		1	NM_000909.6	ENSP00000354652.2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76284 AN: 151652 Hom.: 20827 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.503 AC: 76289 AN: 151768 Hom.: 20824 Cov.: 31 AF XY: 0.502 AC XY: 37236 AN XY: 74156

African (AFR) AF: 0.286 AC: 11849 AN: 41386

American (AMR) AF: 0.584 AC: 8897 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2078 AN: 3466

East Asian (EAS) AF: 0.398 AC: 2045 AN: 5138

South Asian (SAS) AF: 0.587 AC: 2820 AN: 4808

European-Finnish (FIN) AF: 0.479 AC: 5036 AN: 10516

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41635 AN: 67912

Other (OTH) AF: 0.531 AC: 1117 AN: 2102

Alfa AF: 0.553 Hom.: 3017

Bravo AF: 0.499

Asia WGS AF: 0.479 AC: 1666 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.13
DANN	Benign	0.78
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs4057797; hg19: chr4-164245053;