chr14-49893955-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001663.4(ARF6):c.219C>T(p.Leu73=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 1,614,234 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0094 ( 26 hom., cov: 32)
Exomes 𝑓: 0.00098 ( 21 hom. )
Consequence
ARF6
NM_001663.4 synonymous
NM_001663.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.130
Genes affected
ARF6 (HGNC:659): (ADP ribosylation factor 6) This gene encodes a member of the human ARF gene family, which is part of the RAS superfamily. The ARF genes encode small guanine nucleotide-binding proteins that stimulate the ADP-ribosyltransferase activity of cholera toxin and play a role in vesicular trafficking and as activators of phospholipase D. The product of this gene is localized to the plasma membrane, and regulates vesicular trafficking, remodelling of membrane lipids, and signaling pathways that lead to actin remodeling. A pseudogene of this gene is located on chromosome 7. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 14-49893955-C-T is Benign according to our data. Variant chr14-49893955-C-T is described in ClinVar as [Benign]. Clinvar id is 784283.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.13 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00939 (1430/152344) while in subpopulation AFR AF= 0.0322 (1338/41568). AF 95% confidence interval is 0.0308. There are 26 homozygotes in gnomad4. There are 677 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1430 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARF6 | NM_001663.4 | c.219C>T | p.Leu73= | synonymous_variant | 2/2 | ENST00000298316.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARF6 | ENST00000298316.7 | c.219C>T | p.Leu73= | synonymous_variant | 2/2 | 1 | NM_001663.4 | P1 | |
ARF6 | ENST00000693319.1 | c.219C>T | p.Leu73= | synonymous_variant | 1/1 | P1 | |||
ARF6 | ENST00000692608.1 | c.-15-154C>T | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.00934 AC: 1422AN: 152226Hom.: 24 Cov.: 32
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GnomAD3 exomes AF: 0.00248 AC: 623AN: 251356Hom.: 7 AF XY: 0.00185 AC XY: 251AN XY: 135880
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GnomAD4 exome AF: 0.000976 AC: 1427AN: 1461890Hom.: 21 Cov.: 31 AF XY: 0.000828 AC XY: 602AN XY: 727246
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GnomAD4 genome AF: 0.00939 AC: 1430AN: 152344Hom.: 26 Cov.: 32 AF XY: 0.00909 AC XY: 677AN XY: 74494
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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 | Invitae | Dec 31, 2019 | - - |
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