7-98617688-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002523.3(NPTX2):c.227C>T(p.Thr76Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000891 in 1,458,432 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002523.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152092Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000536 AC: 7AN: 1306340Hom.: 0 Cov.: 31 AF XY: 0.00000623 AC XY: 4AN XY: 642386
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.227C>T (p.T76M) alteration is located in exon 1 (coding exon 1) of the NPTX2 gene. This alteration results from a C to T substitution at nucleotide position 227, causing the threonine (T) at amino acid position 76 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