chr4-105895659-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001033047.3(NPNT):āc.7T>Gā(p.Phe3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,551,038 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 (ā ).
Frequency
Consequence
NM_001033047.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPNT | NM_001033047.3 | c.7T>G | p.Phe3Val | missense_variant | 1/12 | ENST00000379987.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPNT | ENST00000379987.7 | c.7T>G | p.Phe3Val | missense_variant | 1/12 | 1 | NM_001033047.3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152084Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000258 AC: 4AN: 155228Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82374
GnomAD4 exome AF: 0.0000150 AC: 21AN: 1398954Hom.: 0 Cov.: 30 AF XY: 0.0000101 AC XY: 7AN XY: 690052
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152084Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.7T>G (p.F3V) alteration is located in exon 1 (coding exon 1) of the NPNT gene. This alteration results from a T to G substitution at nucleotide position 7, causing the phenylalanine (F) at amino acid position 3 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