chr17-75827986-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_199242.3(UNC13D):āc.3252T>Cā(p.His1084His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00222 in 1,605,004 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_199242.3 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: 0.0120 AC: 1824AN: 152208Hom.: 38 Cov.: 33
GnomAD3 exomes AF: 0.00283 AC: 642AN: 226740Hom.: 15 AF XY: 0.00211 AC XY: 263AN XY: 124418
GnomAD4 exome AF: 0.00120 AC: 1737AN: 1452678Hom.: 24 Cov.: 31 AF XY: 0.00102 AC XY: 740AN XY: 722172
GnomAD4 genome AF: 0.0120 AC: 1821AN: 152326Hom.: 38 Cov.: 33 AF XY: 0.0113 AC XY: 840AN XY: 74476
ClinVar
Submissions by phenotype
Familial hemophagocytic lymphohistiocytosis 3 Benign:2
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. -
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not specified Benign:1
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not provided Benign:1
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Autoinflammatory syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at