13-113115754-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_019616.4(F7):c.459C>T(p.His153His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,613,076 control chromosomes in the GnomAD database, including 14,626 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_019616.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.127 AC: 19248AN: 152142Hom.: 1328 Cov.: 33
GnomAD3 exomes AF: 0.137 AC: 34334AN: 250174Hom.: 2982 AF XY: 0.146 AC XY: 19798AN XY: 135650
GnomAD4 exome AF: 0.126 AC: 183916AN: 1460816Hom.: 13296 Cov.: 33 AF XY: 0.132 AC XY: 95567AN XY: 726700
GnomAD4 genome AF: 0.126 AC: 19256AN: 152260Hom.: 1330 Cov.: 33 AF XY: 0.126 AC XY: 9374AN XY: 74432
ClinVar
Submissions by phenotype
not specified Benign:3
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not provided Benign:2
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Factor VII deficiency Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at