rs762866535
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_002529.4(NTRK1):c.2047-6T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,612,488 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002529.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTRK1 | NM_002529.4 | c.2047-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000524377.7 | |||
NTRK1 | NM_001007792.1 | c.1939-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
NTRK1 | NM_001012331.2 | c.2029-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTRK1 | ENST00000524377.7 | c.2047-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002529.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152018Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249492Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135234
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1460470Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 726620
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152018Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74260
ClinVar
Submissions by phenotype
Hereditary insensitivity to pain with anhidrosis Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 08, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 24, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 29, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at