chr11-2160774-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000207.3(INS):c.187+11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.988 in 1,610,624 control chromosomes in the GnomAD database, including 787,793 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000207.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.938 AC: 142735AN: 152154Hom.: 67600 Cov.: 35
GnomAD3 exomes AF: 0.984 AC: 242627AN: 246646Hom.: 119691 AF XY: 0.988 AC XY: 132592AN XY: 134236
GnomAD4 exome AF: 0.993 AC: 1448313AN: 1458352Hom.: 720155 Cov.: 62 AF XY: 0.994 AC XY: 720715AN XY: 725112
GnomAD4 genome AF: 0.938 AC: 142824AN: 152272Hom.: 67638 Cov.: 35 AF XY: 0.940 AC XY: 70000AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:2
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Type 2 diabetes mellitus Benign:1
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Hyperproinsulinemia;C1852092:Type 1 diabetes mellitus 2;C3150617:Maturity-onset diabetes of the young type 10;C5394307:Diabetes mellitus, permanent neonatal 4 Benign:1
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Transient Neonatal Diabetes, Dominant/Recessive Benign:1
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Maturity onset diabetes mellitus in young Benign:1
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Autosomal recessive DOPA responsive dystonia Benign:1
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Maturity-onset diabetes of the young type 10 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