5-51389642-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_002202.3(ISL1):c.479-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0051 in 1,606,088 control chromosomes in the GnomAD database, including 236 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002202.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISL1 | NM_002202.3 | c.479-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000230658.12 | |||
ISL1 | XM_011543380.3 | c.287-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISL1 | ENST00000230658.12 | c.479-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002202.3 | P1 | |||
ISL1 | ENST00000511384.1 | c.479-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
ISL1 | ENST00000505475.3 | n.684-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00504 AC: 766AN: 152040Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.00914 AC: 2159AN: 236138Hom.: 72 AF XY: 0.00850 AC XY: 1101AN XY: 129562
GnomAD4 exome AF: 0.00510 AC: 7416AN: 1453934Hom.: 222 Cov.: 31 AF XY: 0.00504 AC XY: 3647AN XY: 723380
GnomAD4 genome AF: 0.00505 AC: 768AN: 152154Hom.: 14 Cov.: 32 AF XY: 0.00588 AC XY: 437AN XY: 74370
ClinVar
Submissions by phenotype
Bladder exstrophy-epispadias-cloacal extrophy complex Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Malformation Genetics, Karolinska Institutet | Sep 30, 2016 | Variant is rare in the European population (gnomAD Non-Finnish Europeans f = 0.2%). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at