rs778162180
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_002506.3(NGF):c.393C>T(p.Gly131Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,622 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 Likely benign (★★).
Frequency
Consequence
NM_002506.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NGF | NM_002506.3 | c.393C>T | p.Gly131Gly | synonymous_variant | Exon 3 of 3 | ENST00000369512.3 | NP_002497.2 | |
NGF | XM_011541518.3 | c.558C>T | p.Gly186Gly | synonymous_variant | Exon 3 of 3 | XP_011539820.1 | ||
NGF | XM_006710663.4 | c.393C>T | p.Gly131Gly | synonymous_variant | Exon 2 of 2 | XP_006710726.1 | ||
NGF-AS1 | NR_157569.1 | n.207+3163G>A | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250898Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135582
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461612Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727088
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152010Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74234
ClinVar
Submissions by phenotype
Congenital sensory neuropathy with selective loss of small myelinated fibers Benign:2
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at