chr5-73773755-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001177693.2(ARHGEF28):c.476-100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 1,144,480 control chromosomes in the GnomAD database, including 4,627 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.061 ( 385 hom., cov: 32)
Exomes 𝑓: 0.085 ( 4242 hom. )
Consequence
ARHGEF28
NM_001177693.2 intron
NM_001177693.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.35
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=-0.86).
BP6
?
Variant 5-73773755-C-T is Benign according to our data. Variant chr5-73773755-C-T is described in ClinVar as [Benign]. Clinvar id is 1222419.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.093 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF28 | NM_001177693.2 | c.476-100C>T | intron_variant | ENST00000513042.7 | |||
ARHGEF28 | NM_001080479.3 | c.476-100C>T | intron_variant | ||||
ARHGEF28 | NM_001388076.1 | c.182-100C>T | intron_variant | ||||
ARHGEF28 | NM_001388078.1 | c.476-100C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF28 | ENST00000513042.7 | c.476-100C>T | intron_variant | 5 | NM_001177693.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0610 AC: 9274AN: 152128Hom.: 386 Cov.: 32
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GnomAD4 exome AF: 0.0850 AC: 84379AN: 992234Hom.: 4242 AF XY: 0.0850 AC XY: 41508AN XY: 488096
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GnomAD4 genome ? AF: 0.0609 AC: 9272AN: 152246Hom.: 385 Cov.: 32 AF XY: 0.0598 AC XY: 4454AN XY: 74440
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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