rs12512687

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

NPY5R (HGNC:):

ACMG classification

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/exons	MANE	UniProt
NPY5R	XM_005263038.4	c.*433G>A		3_prime_UTR_variant	4/4
NPY5R	XM_011532017.3	c.*433G>A		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

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.: 33 AF XY: 0.0814 AC XY: 6046 AN XY: 74320

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.: 26

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

Other links and lift over

dbSNP: rs12512687; hg19: chr4-164273196;