20-48922217-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -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
Publications
0 publications found
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]
ARFGEF2 Gene-Disease associations (from GenCC):
- periventricular heterotopia with microcephaly, autosomal recessiveInheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen
- periventricular nodular heterotopiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 6 AR,AD gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARFGEF2 | NM_006420.3 | c.121+207C>T | intron_variant | Intron 1 of 38 | ENST00000371917.5 | NP_006411.2 | ||
ARFGEF2 | NM_001410846.1 | c.121+207C>T | intron_variant | Intron 1 of 38 | NP_001397775.1 | |||
ARFGEF2 | XM_047439832.1 | c.-289+207C>T | intron_variant | Intron 1 of 36 | XP_047295788.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00638 AC: 971AN: 152232Hom.: 6 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
971
AN:
152232
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
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 show subpopulations
GnomAD4 genome
AF:
AC:
969
AN:
152350
Hom.:
Cov.:
32
AF XY:
AC XY:
453
AN XY:
74500
show subpopulations
African (AFR)
AF:
AC:
64
AN:
41594
American (AMR)
AF:
AC:
42
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
AC:
39
AN:
3470
East Asian (EAS)
AF:
AC:
2
AN:
5178
South Asian (SAS)
AF:
AC:
111
AN:
4828
European-Finnish (FIN)
AF:
AC:
90
AN:
10624
Middle Eastern (MID)
AF:
AC:
8
AN:
294
European-Non Finnish (NFE)
AF:
AC:
597
AN:
68026
Other (OTH)
AF:
AC:
16
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
52
103
155
206
258
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
28
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 17, 2018
GeneDx
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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