17-80471755-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1BS2
The NM_002522.4(NPTX1):c.1054G>A(p.Val352Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,612,756 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPTX1 | ENST00000306773.5 | c.1054G>A | p.Val352Met | missense_variant | Exon 4 of 5 | 1 | NM_002522.4 | ENSP00000307549.4 | ||
NPTX1 | ENST00000571100.2 | c.340G>A | p.Val114Met | missense_variant | Exon 3 of 4 | 4 | ENSP00000511957.1 | |||
NPTX1 | ENST00000535681.1 | n.1656G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 | |||||
NPTX1 | ENST00000695485.1 | n.477G>A | non_coding_transcript_exon_variant | Exon 3 of 4 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152258Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249302Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135078
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1460498Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 39AN XY: 726592
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152258Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74390
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1054G>A (p.V352M) alteration is located in exon 4 (coding exon 4) of the NPTX1 gene. This alteration results from a G to A substitution at nucleotide position 1054, causing the valine (V) at amino acid position 352 to be replaced by a methionine (M). 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