17-80475708-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002522.4(NPTX1):c.455G>T(p.Arg152Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,610,240 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 (★).
Frequency
Consequence
NM_002522.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPTX1 | ENST00000306773.5 | c.455G>T | p.Arg152Leu | missense_variant | Exon 2 of 5 | 1 | NM_002522.4 | ENSP00000307549.4 | ||
NPTX1 | ENST00000571100.2 | c.-260G>T | 5_prime_UTR_variant | Exon 1 of 4 | 4 | ENSP00000511957.1 | ||||
NPTX1 | ENST00000575212.1 | n.244G>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248226Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134778
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1458030Hom.: 0 Cov.: 31 AF XY: 0.0000207 AC XY: 15AN XY: 725426
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74362
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.455G>T (p.R152L) alteration is located in exon 2 (coding exon 2) of the NPTX1 gene. This alteration results from a G to T substitution at nucleotide position 455, causing the arginine (R) at amino acid position 152 to be replaced by a leucine (L). 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