chr7-24291651-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000905.4(NPY):c.270-12T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,776 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: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
NPY
NM_000905.4 splice_polypyrimidine_tract, intron
NM_000905.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.01136
2
Clinical Significance
Conservation
PhyloP100: 1.15
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 7-24291651-T-C is Benign according to our data. Variant chr7-24291651-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2959043.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPY | NM_000905.4 | c.270-12T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000242152.7 | |||
LOC107986777 | XR_001745132.2 | n.209+27706A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPY | ENST00000242152.7 | c.270-12T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000905.4 | P1 | |||
NPY | ENST00000405982.1 | c.270-12T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
NPY | ENST00000407573.5 | c.270-12T>C | splice_polypyrimidine_tract_variant, intron_variant | 3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461776Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727188
GnomAD4 exome
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AC:
6
AN:
1461776
Hom.:
Cov.:
30
AF XY:
AC XY:
3
AN XY:
727188
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
Bravo
AF:
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 | Aug 02, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at