chr1-156873862-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002529.4(NTRK1):āc.1080G>Cā(p.Thr360=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 1,450,778 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 (ā ). 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTRK1 | NM_002529.4 | c.1080G>C | p.Thr360= | synonymous_variant | 8/17 | ENST00000524377.7 | |
NTRK1 | NM_001012331.2 | c.1080G>C | p.Thr360= | synonymous_variant | 8/16 | ||
NTRK1 | NM_001007792.1 | c.990G>C | p.Thr330= | synonymous_variant | 9/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTRK1 | ENST00000524377.7 | c.1080G>C | p.Thr360= | synonymous_variant | 8/17 | 1 | NM_002529.4 | P4 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000131 AC: 3AN: 228972Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 124100
GnomAD4 exome AF: 0.0000152 AC: 22AN: 1450778Hom.: 0 Cov.: 32 AF XY: 0.0000125 AC XY: 9AN XY: 720746
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Hereditary insensitivity to pain with anhidrosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at