10-70255495-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022146.5(NPFFR1):c.755G>T(p.Gly252Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000588 in 1,547,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022146.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPFFR1 | NM_022146.5 | c.755G>T | p.Gly252Val | missense_variant | 4/4 | ENST00000277942.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPFFR1 | ENST00000277942.7 | c.755G>T | p.Gly252Val | missense_variant | 4/4 | 5 | NM_022146.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151958Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000523 AC: 76AN: 145384Hom.: 0 AF XY: 0.000447 AC XY: 35AN XY: 78330
GnomAD4 exome AF: 0.0000580 AC: 81AN: 1395512Hom.: 0 Cov.: 39 AF XY: 0.0000567 AC XY: 39AN XY: 687858
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 151958Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74212
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 01, 2022 | The c.755G>T (p.G252V) alteration is located in exon 4 (coding exon 4) of the NPFFR1 gene. This alteration results from a G to T substitution at nucleotide position 755, causing the glycine (G) at amino acid position 252 to be replaced by a valine (V). 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