16-18794363-T-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000304414.12(ARL6IP1):c.493+236A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0867 in 152,300 control chromosomes in the GnomAD database, including 691 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.087 ( 691 hom., cov: 33)
Consequence
ARL6IP1
ENST00000304414.12 intron
ENST00000304414.12 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.702
Genes affected
ARL6IP1 (HGNC:697): (ADP ribosylation factor like GTPase 6 interacting protein 1) This gene belongs to the ARL6ip family and encodes a transmembrane protein that is predominantly localized to intracytoplasmic membranes. It is highly expressed in early myeloid progenitor cells and thought to be involved in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. Mutations in this gene are associated with spastic paraplegia 61 (SPG61). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2015]
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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=-0.81).
BP6
Variant 16-18794363-T-G is Benign according to our data. Variant chr16-18794363-T-G is described in ClinVar as [Benign]. Clinvar id is 1293268.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARL6IP1 | NM_015161.3 | c.493+236A>C | intron_variant | ENST00000304414.12 | NP_055976.1 | |||
ARL6IP1 | NM_001313858.1 | c.406+236A>C | intron_variant | NP_001300787.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARL6IP1 | ENST00000304414.12 | c.493+236A>C | intron_variant | 1 | NM_015161.3 | ENSP00000306788 | P1 | |||
ARL6IP1 | ENST00000563861.5 | c.*75+236A>C | intron_variant, NMD_transcript_variant | 1 | ENSP00000456596 | |||||
ARL6IP1 | ENST00000546206.6 | c.406+236A>C | intron_variant | 2 | ENSP00000440048 | |||||
ARL6IP1 | ENST00000562819.5 | c.149-993A>C | intron_variant | 5 | ENSP00000457372 |
Frequencies
GnomAD3 genomes AF: 0.0867 AC: 13193AN: 152182Hom.: 690 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0867 AC: 13203AN: 152300Hom.: 691 Cov.: 33 AF XY: 0.0838 AC XY: 6240AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
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