5-51389734-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_002202.3(ISL1):c.567C>T(p.Asn189=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0064 in 1,614,118 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0044 ( 7 hom., cov: 32)
Exomes 𝑓: 0.0066 ( 47 hom. )
Consequence
ISL1
NM_002202.3 synonymous
NM_002202.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0490
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 -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 5-51389734-C-T is Benign according to our data. Variant chr5-51389734-C-T is described in ClinVar as [Benign]. Clinvar id is 778320.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.049 with no splicing effect.
BS2
High AC in GnomAd4 at 663 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISL1 | NM_002202.3 | c.567C>T | p.Asn189= | synonymous_variant | 4/6 | ENST00000230658.12 | |
ISL1 | XM_011543380.3 | c.375C>T | p.Asn125= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISL1 | ENST00000230658.12 | c.567C>T | p.Asn189= | synonymous_variant | 4/6 | 1 | NM_002202.3 | P1 | |
ISL1 | ENST00000511384.1 | c.567C>T | p.Asn189= | synonymous_variant | 4/6 | 5 | |||
ISL1 | ENST00000505475.3 | n.772C>T | non_coding_transcript_exon_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00437 AC: 665AN: 152162Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00570 AC: 1430AN: 251096Hom.: 8 AF XY: 0.00622 AC XY: 844AN XY: 135798
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GnomAD4 exome AF: 0.00662 AC: 9672AN: 1461838Hom.: 47 Cov.: 34 AF XY: 0.00677 AC XY: 4924AN XY: 727216
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GnomAD4 genome AF: 0.00435 AC: 663AN: 152280Hom.: 7 Cov.: 32 AF XY: 0.00414 AC XY: 308AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at