chr5-51384593-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_002202.3(ISL1):c.81G>A(p.Gln27=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000274 in 1,461,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
ISL1
NM_002202.3 synonymous
NM_002202.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 6.78
Genes affected
ISL1 (HGNC:6132): (ISL LIM homeobox 1) This gene encodes a member of the LIM/homeodomain family of transcription factors. The encoded protein binds to the enhancer region of the insulin gene, among others, and may play an important role in regulating insulin gene expression. The encoded protein is central to the development of pancreatic cell lineages and may also be required for motor neuron generation. Mutations in this gene have been associated with maturity-onset diabetes of the young. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 5-51384593-G-A is Benign according to our data. Variant chr5-51384593-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3349933.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| ISL1 | NM_002202.3 | c.81G>A | p.Gln27= | synonymous_variant | 2/6 | ENST00000230658.12 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ISL1 | ENST00000230658.12 | c.81G>A | p.Gln27= | synonymous_variant | 2/6 | 1 | NM_002202.3 | P1 | |
| ISL1 | ENST00000511384.1 | c.81G>A | p.Gln27= | synonymous_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249572Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135402
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727230
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GnomAD4 genome
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ISL1-related disorder Benign:1
| Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 17, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at