rs2274498
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002529.4(NTRK1):c.1080G>A(p.Thr360Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,603,020 control chromosomes in the GnomAD database, including 38 homozygotes. 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. T360T) has been classified as Likely benign.
Frequency
Consequence
NM_002529.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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NTRK1 | NM_002529.4 | c.1080G>A | p.Thr360Thr | synonymous_variant | Exon 8 of 17 | ENST00000524377.7 | NP_002520.2 | |
NTRK1 | NM_001012331.2 | c.1080G>A | p.Thr360Thr | synonymous_variant | Exon 8 of 16 | NP_001012331.1 | ||
NTRK1 | NM_001007792.1 | c.990G>A | p.Thr330Thr | synonymous_variant | Exon 9 of 17 | NP_001007793.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00139 AC: 212AN: 152126Hom.: 6 Cov.: 31
GnomAD3 exomes AF: 0.00319 AC: 731AN: 228972Hom.: 12 AF XY: 0.00301 AC XY: 373AN XY: 124100
GnomAD4 exome AF: 0.00109 AC: 1585AN: 1450776Hom.: 32 Cov.: 32 AF XY: 0.00113 AC XY: 811AN XY: 720746
GnomAD4 genome AF: 0.00139 AC: 212AN: 152244Hom.: 6 Cov.: 31 AF XY: 0.00165 AC XY: 123AN XY: 74438
ClinVar
Submissions by phenotype
Hereditary insensitivity to pain with anhidrosis Benign:5
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at