rs6857715
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000511017.6(NPY2R-AS1):n.323G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NPY2R-AS1
ENST00000511017.6 non_coding_transcript_exon
ENST00000511017.6 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.69
Genes affected
NPY2R-AS1 (HGNC:55549): (NPY2R antisense RNA 1)
MAP9-AS1 (HGNC:56110): (MAP9 antisense RNA 1)
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPY2R-AS1 | XR_001741894.2 | n.143G>T | non_coding_transcript_exon_variant | 1/2 | |||
NPY2R | NM_001375470.1 | c.-48-5862C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPY2R-AS1 | ENST00000511017.6 | n.323G>T | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
MAP9-AS1 | ENST00000630664.2 | n.208+33746C>A | intron_variant, non_coding_transcript_variant | 5 | |||||
NPY2R-AS1 | ENST00000508687.1 | n.213G>T | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 168Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 128
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
168
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
128
Gnomad4 AFR exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at