rs7965910
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017988.6(SCYL2):c.177+35C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,530,252 control chromosomes in the GnomAD database, including 32,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.22 ( 4337 hom., cov: 32)
Exomes 𝑓: 0.20 ( 27985 hom. )
Consequence
SCYL2
NM_017988.6 intron
NM_017988.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.35
Genes affected
SCYL2 (HGNC:19286): (SCY1 like pseudokinase 2) The protein encoded by this gene associates with clathrin-coated complexes at the plasma membrane and with endocytic coated vesicles. The encoded protein phosphorylates the beta2 subunit of the plasma membrane adapter complex AP2 and interacts with clathrin, showing involvement in clathrin-dependent pathways between the trans-Golgi network and the endosomal system. In addition, this protein has a role in the Wnt signaling pathway by targeting frizzled 5 (Fzd5) for lysosomal degradation. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 12-100283182-C-A is Benign according to our data. Variant chr12-100283182-C-A is described in ClinVar as [Benign]. Clinvar id is 1332927.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.225 AC: 34121AN: 151944Hom.: 4321 Cov.: 32
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GnomAD3 exomes AF: 0.176 AC: 34725AN: 197368Hom.: 3553 AF XY: 0.174 AC XY: 18536AN XY: 106792
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GnomAD4 exome AF: 0.196 AC: 270221AN: 1378190Hom.: 27985 Cov.: 24 AF XY: 0.194 AC XY: 132265AN XY: 681926
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GnomAD4 genome AF: 0.225 AC: 34188AN: 152062Hom.: 4337 Cov.: 32 AF XY: 0.218 AC XY: 16169AN XY: 74340
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Arthrogryposis multiplex congenita 4, neurogenic, with agenesis of the corpus callosum Benign:1
Jul 15, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at