10-46461918-A-G

Position:

• chr10-46461918-A-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4 BP6_Moderate

The ENST00000374312.5(NPY4R):​c.718T>C​(p.Cys240Arg) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 2)
  • Exomes 𝑓: 0.026 (11459 hom.)
  • Failed GnomAD Quality Control
• Consequence: NPY4R ENST00000374312.5 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 5.35

Genes affected

NPY4R (HGNC:9329): (neuropeptide Y receptor Y4) Enables pancreatic polypeptide receptor activity and peptide hormone binding activity. Involved in G protein-coupled receptor signaling pathway. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.351919).
• BP6: Variant 10-46461918-A-G is Benign according to our data. Variant chr10-46461918-A-G is described in ClinVar as [Benign]. Clinvar id is 768358.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPY4R	NM_005972.6	c.718T>C	p.Cys240Arg	missense_variant	3/3	ENST00000374312.5	NP_005963.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPY4R	ENST00000374312.5	c.718T>C	p.Cys240Arg	missense_variant	3/3	1	NM_005972.6	ENSP00000363431	P1
NPY4R	ENST00000612632.3	c.718T>C	p.Cys240Arg	missense_variant	2/2	1		ENSP00000480883	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 91 AN: 65890 Hom.: 0 Cov.: 2 FAILED QC

Gnomad AFR AF: 0.00194

Gnomad AMI AF: 0.00392

Gnomad AMR AF: 0.000649

Gnomad ASJ AF: 0.00198

Gnomad EAS AF: 0.000929

Gnomad SAS AF: 0.00193

Gnomad FIN AF: 0.000438

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00147

Gnomad OTH AF: 0.00216

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0261 AC: 23306 AN: 892952 Hom.: 11459 Cov.: 22 AF XY: 0.0262 AC XY: 11648 AN XY: 445158

Gnomad4 AFR exome AF: 0.248

Gnomad4 AMR exome AF: 0.0420

Gnomad4 ASJ exome AF: 0.0597

Gnomad4 EAS exome AF: 0.00423

Gnomad4 SAS exome AF: 0.0180

Gnomad4 FIN exome AF: 0.0445

Gnomad4 NFE exome AF: 0.0220

Gnomad4 OTH exome AF: 0.0399

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00138 AC: 91 AN: 65916 Hom.: 0 Cov.: 2 AF XY: 0.00103 AC XY: 33 AN XY: 32190

Gnomad4 AFR AF: 0.00194

Gnomad4 AMR AF: 0.000647

Gnomad4 ASJ AF: 0.00198

Gnomad4 EAS AF: 0.000932

Gnomad4 SAS AF: 0.00193

Gnomad4 FIN AF: 0.000438

Gnomad4 NFE AF: 0.00147

Gnomad4 OTH AF: 0.00211

Alfa AF: 0.181 Hom.: 203

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
CADD	Benign	14
MetaRNN	Benign	0.35	T;T
Sift4G	Benign	1.0	T;T
Vest4		0.25
gMVP		0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1352903918; hg19: -;