4-163348082-G-T

Variant names:

• chr4-163348082-G-T
• rs7679206
• NM_006174.4:c.-10+560G>T

Variant summary

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

The NM_006174.4(NPY5R):​c.-10+560G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,948 control chromosomes in the GnomAD database, including 7,179 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 0.30 (7179 hom., cov: 32)
• Consequence: NPY5R NM_006174.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY5R	NM_006174.4	c.-10+560G>T		intron_variant	Intron 3 of 3	ENST00000338566.8	NP_006165.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY5R	ENST00000338566.8	c.-10+560G>T		intron_variant	Intron 3 of 3	1	NM_006174.4	ENSP00000339377.3
NPY5R	ENST00000515560.1	c.-10+560G>T		intron_variant	Intron 3 of 3	2		ENSP00000423917.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45388 AN: 151830 Hom.: 7165 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.299 AC: 45438 AN: 151948 Hom.: 7179 Cov.: 32 AF XY: 0.303 AC XY: 22463 AN XY: 74244

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.315

Alfa AF: 0.285 Hom.: 1053

Bravo AF: 0.303

Asia WGS AF: 0.445 AC: 1545 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.25

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: rs7679206; hg19: chr4-164269234;