1-6462184-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003790.3(TNFRSF25):c.745-10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 1,595,928 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003790.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00195 AC: 297AN: 152124Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00123 AC: 293AN: 237744Hom.: 1 AF XY: 0.00122 AC XY: 157AN XY: 128796
GnomAD4 exome AF: 0.00218 AC: 3143AN: 1443686Hom.: 7 Cov.: 31 AF XY: 0.00207 AC XY: 1480AN XY: 716592
GnomAD4 genome AF: 0.00195 AC: 297AN: 152242Hom.: 2 Cov.: 32 AF XY: 0.00173 AC XY: 129AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
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TNFRSF25-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at