4-155214593-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000910.4(NPY2R):c.654C>T(p.Val218Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. V218V) has been classified as Benign.
Frequency
Consequence
NM_000910.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPY2R | NM_000910.4 | c.654C>T | p.Val218Val | synonymous_variant | Exon 2 of 2 | ENST00000329476.4 | NP_000901.1 | |
NPY2R | NM_001370180.1 | c.654C>T | p.Val218Val | synonymous_variant | Exon 2 of 2 | NP_001357109.1 | ||
NPY2R | NM_001375470.1 | c.654C>T | p.Val218Val | synonymous_variant | Exon 2 of 2 | NP_001362399.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPY2R | ENST00000329476.4 | c.654C>T | p.Val218Val | synonymous_variant | Exon 2 of 2 | 1 | NM_000910.4 | ENSP00000332591.3 | ||
NPY2R | ENST00000506608.1 | c.654C>T | p.Val218Val | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000426366.1 | |||
MAP9-AS1 | ENST00000630664.2 | n.208+40309C>T | intron_variant | Intron 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 42
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at