15-90266349-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001033088.3(NGRN):c.226C>A(p.Pro76Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001033088.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NGRN | ENST00000379095.5 | c.226C>A | p.Pro76Thr | missense_variant | Exon 2 of 3 | 1 | NM_001033088.3 | ENSP00000368389.4 | ||
ENSG00000275674 | ENST00000622269.1 | c.31C>A | p.Pro11Thr | missense_variant | Exon 1 of 4 | 3 | ENSP00000479373.1 | |||
ENSG00000261147 | ENST00000561573.1 | n.*1850C>A | non_coding_transcript_exon_variant | Exon 12 of 13 | 2 | ENSP00000456615.1 | ||||
ENSG00000261147 | ENST00000561573.1 | n.*1850C>A | 3_prime_UTR_variant | Exon 12 of 13 | 2 | ENSP00000456615.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250118Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135456
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461660Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 727100
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.226C>A (p.P76T) alteration is located in exon 2 (coding exon 2) of the NGRN gene. This alteration results from a C to A substitution at nucleotide position 226, causing the proline (P) at amino acid position 76 to be replaced by a threonine (T). 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