rs80356676
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_002529.4(NTRK1):βc.1860_1861insTβ(p.Pro621SerfsTer12) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,070 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Pathogenic (β β ). Synonymous variant affecting the same amino acid position (i.e. G620G) has been classified as Benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_002529.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTRK1 | NM_002529.4 | c.1860_1861insT | p.Pro621SerfsTer12 | frameshift_variant | 15/17 | ENST00000524377.7 | NP_002520.2 | |
NTRK1 | NM_001007792.1 | c.1752_1753insT | p.Pro585SerfsTer12 | frameshift_variant | 15/17 | NP_001007793.1 | ||
NTRK1 | NM_001012331.2 | c.1842_1843insT | p.Pro615SerfsTer12 | frameshift_variant | 14/16 | NP_001012331.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NTRK1 | ENST00000524377.7 | c.1860_1861insT | p.Pro621SerfsTer12 | frameshift_variant | 15/17 | 1 | NM_002529.4 | ENSP00000431418 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152088Hom.: 1 Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460864Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726718
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152206Hom.: 1 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74434
ClinVar
Submissions by phenotype
Hereditary insensitivity to pain with anhidrosis Pathogenic:6Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | May 03, 2023 | Criteria applied: PVS1,PM3_STR,PM2_SUP - |
Pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
not provided, no classification provided | literature only | GeneReviews | - | Founder variant in Israeli Bedouins - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 01, 2021 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | 3billion | Sep 01, 2022 | The variant is not observed in the gnomAD v2.1.1 dataset. Frameshift variant is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000021306 / PMID: 10861667). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 19, 2000 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 05, 2019 | This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported as disease-causing in multiple individuals [PMID: 18955016, 10861667, 28328124, ClinVar ID: 21306] - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 03, 2022 | Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 34405299, 28328124, 18955016, 10861667, 31841741, 32056211, 20301726, 34732685) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at