chr15-76381375-T-C
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_020843.4(SCAPER):c.3705+3A>G variant causes a splice donor region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.345 in 1,607,546 control chromosomes in the GnomAD database, including 99,181 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.33 ( 8537 hom., cov: 32)
Exomes 𝑓: 0.35 ( 90644 hom. )
Consequence
SCAPER
NM_020843.4 splice_donor_region, intron
NM_020843.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.9662
1
1
Clinical Significance
Conservation
PhyloP100: 7.36
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 15-76381375-T-C is Benign according to our data. Variant chr15-76381375-T-C is described in ClinVar as [Benign]. Clinvar id is 1327980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-76381375-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAPER | NM_020843.4 | c.3705+3A>G | splice_donor_region_variant, intron_variant | ENST00000563290.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAPER | ENST00000563290.6 | c.3705+3A>G | splice_donor_region_variant, intron_variant | 5 | NM_020843.4 | P1 | |||
SCAPER | ENST00000324767.11 | c.3705+3A>G | splice_donor_region_variant, intron_variant | 1 | P1 | ||||
SCAPER | ENST00000538941.6 | c.2967+3A>G | splice_donor_region_variant, intron_variant | 1 | |||||
SCAPER | ENST00000303521.10 | n.3772A>G | non_coding_transcript_exon_variant | 27/27 | 2 |
Frequencies
GnomAD3 genomes AF: 0.327 AC: 49781AN: 152006Hom.: 8526 Cov.: 32
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GnomAD3 exomes AF: 0.371 AC: 89798AN: 242194Hom.: 17564 AF XY: 0.377 AC XY: 49391AN XY: 131118
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GnomAD4 exome AF: 0.346 AC: 504060AN: 1455422Hom.: 90644 Cov.: 32 AF XY: 0.351 AC XY: 254190AN XY: 723632
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GnomAD4 genome AF: 0.328 AC: 49824AN: 152124Hom.: 8537 Cov.: 32 AF XY: 0.331 AC XY: 24577AN XY: 74360
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Intellectual developmental disorder and retinitis pigmentosa; IDDRP Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
SCAPER-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as 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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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at