chr1-156868259-G-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002529.4(NTRK1):c.574+10G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,454,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002529.4 intron
Scores
Clinical Significance
Conservation
Publications
- hereditary sensory and autonomic neuropathy type 4Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)
- familial medullary thyroid carcinomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTRK1 | NM_002529.4 | c.574+10G>T | intron_variant | Intron 5 of 16 | ENST00000524377.7 | NP_002520.2 | ||
NTRK1 | NM_001012331.2 | c.574+10G>T | intron_variant | Intron 5 of 15 | NP_001012331.1 | |||
NTRK1 | NM_001007792.1 | c.484+10G>T | intron_variant | Intron 6 of 16 | NP_001007793.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1454184Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 723682 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at