chr4-163326401-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000909.6(NPY1R):c.154A>T(p.Ile52Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000909.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPY1R | NM_000909.6 | c.154A>T | p.Ile52Phe | missense_variant | 2/3 | ENST00000296533.3 | |
NPY1R | XM_005263031.5 | c.154A>T | p.Ile52Phe | missense_variant | 2/3 | ||
NPY1R | XM_011532010.4 | c.154A>T | p.Ile52Phe | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPY1R | ENST00000296533.3 | c.154A>T | p.Ile52Phe | missense_variant | 2/3 | 1 | NM_000909.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251136Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135722
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727190
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.154A>T (p.I52F) alteration is located in exon 2 (coding exon 1) of the NPY1R gene. This alteration results from a A to T substitution at nucleotide position 154, causing the isoleucine (I) at amino acid position 52 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at