NM_002529.4:c.2142C>T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_002529.4(NTRK1):c.2142C>T(p.Gly714Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000992 in 1,613,404 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_002529.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTRK1 | NM_002529.4 | c.2142C>T | p.Gly714Gly | synonymous_variant | Exon 16 of 17 | ENST00000524377.7 | NP_002520.2 | |
NTRK1 | NM_001012331.2 | c.2124C>T | p.Gly708Gly | synonymous_variant | Exon 15 of 16 | NP_001012331.1 | ||
NTRK1 | NM_001007792.1 | c.2034C>T | p.Gly678Gly | synonymous_variant | Exon 16 of 17 | NP_001007793.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000613 AC: 93AN: 151598Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000171 AC: 43AN: 251224Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135832
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461688Hom.: 0 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727146
GnomAD4 genome AF: 0.000613 AC: 93AN: 151716Hom.: 0 Cov.: 30 AF XY: 0.000674 AC XY: 50AN XY: 74136
ClinVar
Submissions by phenotype
Hereditary insensitivity to pain with anhidrosis Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at