chr4-163350687-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_006174.4(NPY5R):c.414C>T(p.Val138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 1,613,798 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00065 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 2 hom. )
Consequence
NPY5R
NM_006174.4 synonymous
NM_006174.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.335
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 4-163350687-C-T is Benign according to our data. Variant chr4-163350687-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 746358.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.335 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPY5R | NM_006174.4 | c.414C>T | p.Val138= | synonymous_variant | 4/4 | ENST00000338566.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPY5R | ENST00000338566.8 | c.414C>T | p.Val138= | synonymous_variant | 4/4 | 1 | NM_006174.4 | P1 | |
NPY5R | ENST00000506953.1 | c.414C>T | p.Val138= | synonymous_variant | 1/1 | P1 | |||
NPY5R | ENST00000515560.1 | c.414C>T | p.Val138= | synonymous_variant | 4/4 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000651 AC: 99AN: 152174Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000768 AC: 193AN: 251266Hom.: 0 AF XY: 0.000744 AC XY: 101AN XY: 135790
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GnomAD4 exome AF: 0.00114 AC: 1672AN: 1461506Hom.: 2 Cov.: 33 AF XY: 0.00115 AC XY: 839AN XY: 727078
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GnomAD4 genome ? AF: 0.000650 AC: 99AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74452
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2018 | - - |
Computational scores
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at