NM_001048166.1:c.3786G>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001048166.1(STIL):c.3786G>A(p.Thr1262Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00707 in 1,612,162 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001048166.1 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: 0.00512 AC: 779AN: 152176Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00742 AC: 1855AN: 250004Hom.: 17 AF XY: 0.00867 AC XY: 1171AN XY: 135064
GnomAD4 exome AF: 0.00727 AC: 10620AN: 1459868Hom.: 74 Cov.: 30 AF XY: 0.00783 AC XY: 5686AN XY: 726054
GnomAD4 genome AF: 0.00512 AC: 779AN: 152294Hom.: 3 Cov.: 33 AF XY: 0.00544 AC XY: 405AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:4
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not specified Benign:2
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Microcephaly 7, primary, autosomal recessive 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at