chr3-3147595-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_182916.3(TRNT1):c.948A>G(p.Ala316Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 1,613,574 control chromosomes in the GnomAD database, including 541,540 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_182916.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNT1 | NM_182916.3 | c.948A>G | p.Ala316Ala | synonymous_variant | Exon 7 of 8 | ENST00000251607.11 | NP_886552.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.742 AC: 112629AN: 151880Hom.: 43370 Cov.: 31
GnomAD3 exomes AF: 0.799 AC: 200214AN: 250614Hom.: 81203 AF XY: 0.810 AC XY: 109941AN XY: 135774
GnomAD4 exome AF: 0.823 AC: 1202908AN: 1461576Hom.: 498155 Cov.: 59 AF XY: 0.825 AC XY: 599669AN XY: 727100
GnomAD4 genome AF: 0.741 AC: 112687AN: 151998Hom.: 43385 Cov.: 31 AF XY: 0.744 AC XY: 55282AN XY: 74316
ClinVar
Submissions by phenotype
not specified Benign:3
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
This variant is classified as Benign based on local population frequency. This variant was detected in 96% of patients studied by a panel of primary immunodeficiencies. Number of patients: 91. Only high quality variants are reported. -
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. -
Congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome Benign:2
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not provided Benign:1Other:1
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Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
Retinitis pigmentosa and erythrocytic microcytosis Benign:1
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Retinal dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at