11-2159830-T-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000207.3(INS):c.*22A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 1,607,734 control chromosomes in the GnomAD database, including 415,760 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000207.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.610 AC: 92705AN: 151854Hom.: 31998 Cov.: 33
GnomAD3 exomes AF: 0.733 AC: 176653AN: 240868Hom.: 67320 AF XY: 0.744 AC XY: 97323AN XY: 130744
GnomAD4 exome AF: 0.720 AC: 1048832AN: 1455762Hom.: 383754 Cov.: 40 AF XY: 0.725 AC XY: 524628AN XY: 723788
GnomAD4 genome AF: 0.610 AC: 92730AN: 151972Hom.: 32006 Cov.: 33 AF XY: 0.623 AC XY: 46299AN XY: 74286
ClinVar
Submissions by phenotype
not provided Benign:2
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Maturity-onset diabetes of the young type 10 Benign:2
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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. -
Diabetes mellitus type 1 Uncertain:1
Potent mutations in this gene can cause early onset diabetes mellitus which is insulin dependent. May have poor response to sulfonylureas, as potent mutations in INS gene can cause beta cell destruction. rs3842753 variant, could be a contributing factor to the increased risk of T1D development, as it might increase insulin production. However more evidence are required to ascertain the role of this particular variant rs3842753 in Type 1 diabetes mellitus . -
Diabetes mellitus, permanent neonatal 4 Benign:1
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Transient Neonatal Diabetes, Dominant/Recessive Benign:1
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Hyperproinsulinemia Benign:1
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Type 1 diabetes mellitus 2 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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at