chrX-70283553-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001363807.1(RAB41):c.384C>T(p.His128=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,095,536 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000055 ( 0 hom. 2 hem. )
Consequence
RAB41
NM_001363807.1 synonymous
NM_001363807.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.622
Genes affected
RAB41 (HGNC:18293): (RAB41, member RAS oncogene family) This gene encodes a small GTP-binding protein that belongs to the largest family within the Ras superfamily. These proteins function as regulators of membrane trafficking. They cycle between inactive GDP-bound and activated GTP-bound states, which is controlled by GTP hydrolysis-activating proteins (GAPs). This family member can be activated by the GAP protein RN-Tre, and it is localized to the Golgi complex. [provided by RefSeq, May 2010]
PDZD11 (HGNC:28034): (PDZ domain containing 11) Enables protein C-terminus binding activity. Involved in pore complex assembly. Located in basolateral plasma membrane and cytosol. Part of pore complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant X-70283553-C-T is Benign according to our data. Variant chrX-70283553-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2660812.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.622 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB41 | NM_001363807.1 | c.384C>T | p.His128= | synonymous_variant | 5/8 | ENST00000374473.6 | |
RAB41 | NM_001032726.3 | c.381C>T | p.His127= | synonymous_variant | 5/8 | ||
RAB41 | XM_011530948.4 | c.384C>T | p.His128= | synonymous_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB41 | ENST00000374473.6 | c.384C>T | p.His128= | synonymous_variant | 5/8 | 5 | NM_001363807.1 | P1 | |
RAB41 | ENST00000276066.4 | c.381C>T | p.His127= | synonymous_variant | 5/8 | 1 | |||
PDZD11 | ENST00000695560.1 | c.*97-1278G>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183382Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67822
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GnomAD4 exome AF: 0.00000548 AC: 6AN: 1095536Hom.: 0 Cov.: 29 AF XY: 0.00000554 AC XY: 2AN XY: 360982
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GnomAD4 genome ? Cov.: 23
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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
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | RAB41: BP4, BP7 - |
Computational scores
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Name
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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