rs747640827
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152383.5(DIS3L2):c.1317+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,455,382 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_152383.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIS3L2 | NM_152383.5 | c.1317+7A>G | splice_region_variant, intron_variant | ENST00000325385.12 | |||
DIS3L2 | NM_001257281.2 | c.1317+7A>G | splice_region_variant, intron_variant | ||||
DIS3L2 | NR_046476.2 | n.1463+7A>G | splice_region_variant, intron_variant, non_coding_transcript_variant | ||||
DIS3L2 | NR_046477.2 | n.1439+7A>G | splice_region_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIS3L2 | ENST00000325385.12 | c.1317+7A>G | splice_region_variant, intron_variant | 5 | NM_152383.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245180Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133078
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1455382Hom.: 0 Cov.: 28 AF XY: 0.00000552 AC XY: 4AN XY: 724218
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Perlman syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at