NM_002529.4:c.1838G>T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1
The NM_002529.4(NTRK1):c.1838G>T(p.Gly613Val) variant causes a missense change. The variant allele was found at a frequency of 0.0533 in 1,613,774 control chromosomes in the GnomAD database, including 2,657 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002529.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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NTRK1 | NM_002529.4 | c.1838G>T | p.Gly613Val | missense_variant | Exon 15 of 17 | ENST00000524377.7 | NP_002520.2 | |
NTRK1 | NM_001012331.2 | c.1820G>T | p.Gly607Val | missense_variant | Exon 14 of 16 | NP_001012331.1 | ||
NTRK1 | NM_001007792.1 | c.1730G>T | p.Gly577Val | missense_variant | Exon 15 of 17 | NP_001007793.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0377 AC: 5726AN: 152068Hom.: 146 Cov.: 32
GnomAD3 exomes AF: 0.0417 AC: 10381AN: 249090Hom.: 291 AF XY: 0.0446 AC XY: 6013AN XY: 134858
GnomAD4 exome AF: 0.0550 AC: 80333AN: 1461588Hom.: 2511 Cov.: 32 AF XY: 0.0554 AC XY: 40280AN XY: 727104
GnomAD4 genome AF: 0.0376 AC: 5723AN: 152186Hom.: 146 Cov.: 32 AF XY: 0.0352 AC XY: 2619AN XY: 74412
ClinVar
Submissions by phenotype
Hereditary insensitivity to pain with anhidrosis Benign:6Other:1
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not specified Benign:6
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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. -
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not provided Benign:3
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Familial medullary thyroid carcinoma Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at