chr10-27504701-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_021252.5(RAB18):c.68+264C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00565 in 696,440 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0038 ( 7 hom., cov: 33)
Exomes 𝑓: 0.0062 ( 38 hom. )
Consequence
RAB18
NM_021252.5 intron
NM_021252.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.719
Genes affected
RAB18 (HGNC:14244): (RAB18, member RAS oncogene family) The protein encoded by this gene is a member of a family of Ras-related small GTPases that regulate membrane trafficking in organelles and transport vesicles. Knockdown studies is zebrafish suggest that this protein may have a role in eye and brain development. Mutations in this gene are associated with Warburg micro syndrome type 3. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 10-27504701-C-T is Benign according to our data. Variant chr10-27504701-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1198375.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0038 (579/152304) while in subpopulation SAS AF= 0.013 (63/4830). AF 95% confidence interval is 0.0105. There are 7 homozygotes in gnomad4. There are 341 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00380 AC: 579AN: 152186Hom.: 7 Cov.: 33
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GnomAD3 exomes AF: 0.00609 AC: 1072AN: 175972Hom.: 13 AF XY: 0.00690 AC XY: 665AN XY: 96418
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GnomAD4 exome AF: 0.00617 AC: 3357AN: 544136Hom.: 38 Cov.: 4 AF XY: 0.00662 AC XY: 1962AN XY: 296376
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GnomAD4 genome AF: 0.00380 AC: 579AN: 152304Hom.: 7 Cov.: 33 AF XY: 0.00458 AC XY: 341AN XY: 74472
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 27, 2019
GeneDx
Significance: Likely 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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at