5-51387821-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002202.3(ISL1):c.478+72T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,581,796 control chromosomes in the GnomAD database, including 121,430 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.44 ( 15664 hom., cov: 33)
Exomes 𝑓: 0.38 ( 105766 hom. )
Consequence
ISL1
NM_002202.3 intron
NM_002202.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.15
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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISL1 | NM_002202.3 | c.478+72T>C | intron_variant | ENST00000230658.12 | |||
ISL1 | XM_011543380.3 | c.286+72T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISL1 | ENST00000230658.12 | c.478+72T>C | intron_variant | 1 | NM_002202.3 | P1 | |||
ISL1 | ENST00000511384.1 | c.478+72T>C | intron_variant | 5 | |||||
ISL1 | ENST00000505475.3 | n.683+72T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.435 AC: 66161AN: 152002Hom.: 15631 Cov.: 33
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GnomAD4 exome AF: 0.380 AC: 543361AN: 1429676Hom.: 105766 AF XY: 0.378 AC XY: 268433AN XY: 711078
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GnomAD4 genome AF: 0.435 AC: 66241AN: 152120Hom.: 15664 Cov.: 33 AF XY: 0.428 AC XY: 31809AN XY: 74358
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at