chr15-90271664-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001033088.3(NGRN):c.752C>T(p.Ala251Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NGRN | ENST00000379095.5 | c.752C>T | p.Ala251Val | missense_variant | Exon 3 of 3 | 1 | NM_001033088.3 | ENSP00000368389.4 | ||
ENSG00000275674 | ENST00000622269.1 | c.80+5266C>T | intron_variant | Intron 1 of 3 | 3 | ENSP00000479373.1 | ||||
ENSG00000261147 | ENST00000561573.1 | n.*2376C>T | non_coding_transcript_exon_variant | Exon 13 of 13 | 2 | ENSP00000456615.1 | ||||
ENSG00000261147 | ENST00000561573.1 | n.*2376C>T | 3_prime_UTR_variant | Exon 13 of 13 | 2 | ENSP00000456615.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251270Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135860
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461874Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727240
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.752C>T (p.A251V) alteration is located in exon 3 (coding exon 3) of the NGRN gene. This alteration results from a C to T substitution at nucleotide position 752, causing the alanine (A) at amino acid position 251 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