NM_006420.3:c.4455-20_4455-19dupTT
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS1
The NM_006420.3(ARFGEF2):c.4455-20_4455-19dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,611,422 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 25)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
ARFGEF2
NM_006420.3 intron
NM_006420.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.151
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0000288 (42/1459768) while in subpopulation AMR AF= 0.0000896 (4/44652). AF 95% confidence interval is 0.0000299. There are 0 homozygotes in gnomad4_exome. There are 15 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARFGEF2 | NM_006420.3 | c.4455-20_4455-19dupTT | intron_variant | Intron 32 of 38 | ENST00000371917.5 | NP_006411.2 | ||
ARFGEF2 | NM_001410846.1 | c.4452-20_4452-19dupTT | intron_variant | Intron 32 of 38 | NP_001397775.1 | |||
ARFGEF2 | XM_047439832.1 | c.3891-20_3891-19dupTT | intron_variant | Intron 30 of 36 | XP_047295788.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151654Hom.: 0 Cov.: 25
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GnomAD4 exome AF: 0.0000288 AC: 42AN: 1459768Hom.: 0 Cov.: 33 AF XY: 0.0000207 AC XY: 15AN XY: 726178
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GnomAD4 genome AF: 0.00000659 AC: 1AN: 151654Hom.: 0 Cov.: 25 AF XY: 0.0000135 AC XY: 1AN XY: 74014
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at