chr10-70255597-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022146.5(NPFFR1):c.653C>T(p.Thr218Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000204 in 1,557,294 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T218A) has been classified as Likely benign.
Frequency
Consequence
NM_022146.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPFFR1 | NM_022146.5 | c.653C>T | p.Thr218Ile | missense_variant | 4/4 | ENST00000277942.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPFFR1 | ENST00000277942.7 | c.653C>T | p.Thr218Ile | missense_variant | 4/4 | 5 | NM_022146.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000495 AC: 8AN: 161572Hom.: 0 AF XY: 0.0000580 AC XY: 5AN XY: 86260
GnomAD4 exome AF: 0.000221 AC: 310AN: 1404984Hom.: 0 Cov.: 40 AF XY: 0.000228 AC XY: 158AN XY: 693548
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.653C>T (p.T218I) alteration is located in exon 4 (coding exon 4) of the NPFFR1 gene. This alteration results from a C to T substitution at nucleotide position 653, causing the threonine (T) at amino acid position 218 to be replaced by an isoleucine (I). 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