chr5-73773756-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001177693.2(ARHGEF28):c.476-99A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 1,143,728 control chromosomes in the GnomAD database, including 183,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.62 ( 30177 hom., cov: 33)
Exomes 𝑓: 0.55 ( 153054 hom. )
Consequence
ARHGEF28
NM_001177693.2 intron
NM_001177693.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.20
Genes affected
ARHGEF28 (HGNC:30322): (Rho guanine nucleotide exchange factor 28) This gene encodes a member of the Rho guanine nucleotide exchange factor family. The encoded protein interacts with low molecular weight neurofilament mRNA and may be involved in the formation of amyotrophic lateral sclerosis neurofilament aggregates. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]
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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=-0.87).
BP6
?
Variant 5-73773756-A-G is Benign according to our data. Variant chr5-73773756-A-G is described in ClinVar as [Benign]. Clinvar id is 1277651.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF28 | NM_001177693.2 | c.476-99A>G | intron_variant | ENST00000513042.7 | |||
ARHGEF28 | NM_001080479.3 | c.476-99A>G | intron_variant | ||||
ARHGEF28 | NM_001388076.1 | c.182-99A>G | intron_variant | ||||
ARHGEF28 | NM_001388078.1 | c.476-99A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF28 | ENST00000513042.7 | c.476-99A>G | intron_variant | 5 | NM_001177693.2 |
Frequencies
GnomAD3 genomes ? AF: 0.619 AC: 94107AN: 152032Hom.: 30122 Cov.: 33
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GnomAD4 exome AF: 0.551 AC: 546787AN: 991578Hom.: 153054 AF XY: 0.550 AC XY: 267843AN XY: 487364
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GnomAD4 genome ? AF: 0.619 AC: 94221AN: 152150Hom.: 30177 Cov.: 33 AF XY: 0.617 AC XY: 45863AN XY: 74372
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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 18, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at