4-163350469-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006174.4(NPY5R):c.196C>T(p.Leu66Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,613,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L66V) has been classified as Uncertain significance.
Frequency
Consequence
NM_006174.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPY5R | ENST00000338566.8 | c.196C>T | p.Leu66Phe | missense_variant | Exon 4 of 4 | 1 | NM_006174.4 | ENSP00000339377.3 | ||
NPY5R | ENST00000506953.1 | c.196C>T | p.Leu66Phe | missense_variant | Exon 1 of 1 | 6 | ENSP00000423474.1 | |||
NPY5R | ENST00000515560.1 | c.196C>T | p.Leu66Phe | missense_variant | Exon 4 of 4 | 2 | ENSP00000423917.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251370Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135862
GnomAD4 exome AF: 0.000150 AC: 219AN: 1461698Hom.: 0 Cov.: 33 AF XY: 0.000131 AC XY: 95AN XY: 727160
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74302
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at