20-48922217-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_006420.3(ARFGEF2):c.121+207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00636 in 152,350 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0064 ( 6 hom., cov: 32)
Consequence
ARFGEF2
NM_006420.3 intron
NM_006420.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.65
Genes affected
ARFGEF2 (HGNC:15853): (ADP ribosylation factor guanine nucleotide exchange factor 2) ADP-ribosylation factors (ARFs) play an important role in intracellular vesicular trafficking. The protein encoded by this gene is involved in the activation of ARFs by accelerating replacement of bound GDP with GTP and is involved in Golgi transport. It contains a Sec7 domain, which may be responsible for its guanine-nucleotide exchange activity and also brefeldin A inhibition. [provided by RefSeq, Jul 2008]
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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=-0.53).
BP6
Variant 20-48922217-C-T is Benign according to our data. Variant chr20-48922217-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1216921.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00636 (969/152350) while in subpopulation SAS AF= 0.023 (111/4828). AF 95% confidence interval is 0.0195. There are 6 homozygotes in gnomad4. There are 453 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARFGEF2 | NM_006420.3 | c.121+207C>T | intron_variant | ENST00000371917.5 | NP_006411.2 | |||
ARFGEF2 | NM_001410846.1 | c.121+207C>T | intron_variant | NP_001397775.1 | ||||
ARFGEF2 | XM_047439832.1 | c.-289+207C>T | intron_variant | XP_047295788.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00638 AC: 971AN: 152232Hom.: 6 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00636 AC: 969AN: 152350Hom.: 6 Cov.: 32 AF XY: 0.00608 AC XY: 453AN XY: 74500
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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 | GeneDx | Jul 17, 2018 | - - |
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