1-115286115-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002506.3(NGF):c.681G>A(p.Thr227=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,246 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 (★). Synonymous variant affecting the same amino acid position (i.e. T227T) has been classified as Likely benign.
Frequency
Consequence
NM_002506.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NGF | NM_002506.3 | c.681G>A | p.Thr227= | synonymous_variant | 3/3 | ENST00000369512.3 | |
NGF-AS1 | NR_157569.1 | n.207+2875C>T | intron_variant, non_coding_transcript_variant | ||||
NGF | XM_011541518.3 | c.846G>A | p.Thr282= | synonymous_variant | 3/3 | ||
NGF | XM_006710663.4 | c.681G>A | p.Thr227= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NGF | ENST00000369512.3 | c.681G>A | p.Thr227= | synonymous_variant | 3/3 | 1 | NM_002506.3 | P1 | |
NGF-AS1 | ENST00000425449.1 | n.207+2875C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151986Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250536Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135418
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1461260Hom.: 0 Cov.: 30 AF XY: 0.0000385 AC XY: 28AN XY: 726838
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151986Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74240
ClinVar
Submissions by phenotype
Congenital sensory neuropathy with selective loss of small myelinated fibers Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 30, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at