chr1-156879176-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002529.4(NTRK1):c.1860C>T(p.Gly620=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00868 in 1,613,056 control chromosomes in the GnomAD database, including 480 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G620G) 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTRK1 | NM_002529.4 | c.1860C>T | p.Gly620= | synonymous_variant | 15/17 | ENST00000524377.7 | |
NTRK1 | NM_001012331.2 | c.1842C>T | p.Gly614= | synonymous_variant | 14/16 | ||
NTRK1 | NM_001007792.1 | c.1752C>T | p.Gly584= | synonymous_variant | 15/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTRK1 | ENST00000524377.7 | c.1860C>T | p.Gly620= | synonymous_variant | 15/17 | 1 | NM_002529.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0317 AC: 4826AN: 152074Hom.: 217 Cov.: 32
GnomAD3 exomes AF: 0.0106 AC: 2632AN: 248998Hom.: 111 AF XY: 0.00857 AC XY: 1156AN XY: 134844
GnomAD4 exome AF: 0.00628 AC: 9173AN: 1460864Hom.: 263 Cov.: 33 AF XY: 0.00564 AC XY: 4101AN XY: 726718
GnomAD4 genome AF: 0.0318 AC: 4834AN: 152192Hom.: 217 Cov.: 32 AF XY: 0.0301 AC XY: 2240AN XY: 74426
ClinVar
Submissions by phenotype
Hereditary insensitivity to pain with anhidrosis Benign:6
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 14, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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. - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 02, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at