Genetic Variant XM_005263038.4:c.*433G>A (chr4-163352044-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Variant links:

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]

NPY5R links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 link	c.*433G>A		downstream_gene_variant		ENST00000338566.8	NP_006165.1	Q15761

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY5R	ENST00000338566.8 link	c.*433G>A		downstream_gene_variant		1	NM_006174.4	ENSP00000339377.3		Q15761
NPY5R	ENST00000515560.1 link	c.*433G>A		downstream_gene_variant		2		ENSP00000423917.1		Q15761

Frequencies

GnomAD3 genomes

AF:

0.0795

AC:

12082

AN:

151930

Hom.:

543

Cov.:

show subpopulations

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.:

AF XY:

0.0817

AC XY:

175

AN XY:

2142

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.100

Gnomad4 ASJ exome

AF:

0.0625

Gnomad4 EAS exome

AF:

0.0625

Gnomad4 SAS exome

AF:

0.286

Gnomad4 FIN exome

AF:

0.0881

Gnomad4 NFE exome

AF:

0.0357

Gnomad4 OTH exome

AF:

0.0500

GnomAD4 genome

AF:

0.0794

AC:

12075

AN:

152048

Hom.:

539

Cov.:

AF XY:

0.0814

AC XY:

6046

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.0772

Gnomad4 AMR

AF:

0.0948

Gnomad4 ASJ

AF:

0.0664

Gnomad4 EAS

AF:

0.141

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.0821

Gnomad4 NFE

AF:

0.0669

Gnomad4 OTH

AF:

0.0747

Alfa

AF:

0.0343

Hom.:

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over