7-24285443-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000242152.7(NPY):c.188+15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000561 in 1,605,226 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000055 ( 0 hom. )
Consequence
NPY
ENST00000242152.7 intron
ENST00000242152.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.490
Genes affected
NPY (HGNC:7955): (neuropeptide Y) This gene encodes a neuropeptide that is widely expressed in the central nervous system and influences many physiological processes, including cortical excitability, stress response, food intake, circadian rhythms, and cardiovascular function. The neuropeptide functions through G protein-coupled receptors to inhibit adenylyl cyclase, activate mitogen-activated protein kinase (MAPK), regulate intracellular calcium levels, and activate potassium channels. A polymorphism in this gene resulting in a change of leucine 7 to proline in the signal peptide is associated with elevated cholesterol levels, higher alcohol consumption, and may be a risk factor for various metabolic and cardiovascular diseases. The protein also exhibits antimicrobial activity against bacteria and fungi. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 7-24285443-G-A is Benign according to our data. Variant chr7-24285443-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1929817.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPY | NM_000905.4 | c.188+15G>A | intron_variant | ENST00000242152.7 | NP_000896.1 | |||
LOC107986777 | XR_001745132.2 | n.209+33914C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPY | ENST00000242152.7 | c.188+15G>A | intron_variant | 1 | NM_000905.4 | ENSP00000242152 | P1 | |||
NPY | ENST00000405982.1 | c.188+15G>A | intron_variant | 1 | ENSP00000385282 | P1 | ||||
NPY | ENST00000407573.5 | c.188+15G>A | intron_variant | 3 | ENSP00000384364 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152150Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000247 AC: 6AN: 242626Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131306
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GnomAD4 exome AF: 0.0000551 AC: 80AN: 1453076Hom.: 0 Cov.: 34 AF XY: 0.0000458 AC XY: 33AN XY: 721032
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74328
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Oct 01, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at