rs3774225
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_021629.4(GNB4):c.*3G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,595,862 control chromosomes in the GnomAD database, including 25,512 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.17 ( 2264 hom., cov: 32)
Exomes 𝑓: 0.18 ( 23248 hom. )
Consequence
GNB4
NM_021629.4 3_prime_UTR
NM_021629.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.809
Genes affected
GNB4 (HGNC:20731): (G protein subunit beta 4) Heterotrimeric guanine nucleotide-binding proteins (G proteins), which integrate signals between receptors and effector proteins, are composed of an alpha, a beta, and a gamma subunit. These subunits are encoded by families of related genes. This gene encodes a beta subunit. Beta subunits are important regulators of alpha subunits, as well as of certain signal transduction receptors and effectors. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
?
Variant 3-179401210-C-T is Benign according to our data. Variant chr3-179401210-C-T is described in ClinVar as [Benign]. Clinvar id is 261426.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-179401210-C-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNB4 | NM_021629.4 | c.*3G>A | 3_prime_UTR_variant | 10/10 | ENST00000232564.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNB4 | ENST00000232564.8 | c.*3G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_021629.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.168 AC: 25573AN: 151944Hom.: 2263 Cov.: 32
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GnomAD3 exomes AF: 0.191 AC: 47755AN: 249404Hom.: 4967 AF XY: 0.190 AC XY: 25577AN XY: 134964
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GnomAD4 exome AF: 0.176 AC: 253401AN: 1443800Hom.: 23248 Cov.: 26 AF XY: 0.176 AC XY: 126713AN XY: 719404
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GnomAD4 genome ? AF: 0.168 AC: 25579AN: 152062Hom.: 2264 Cov.: 32 AF XY: 0.171 AC XY: 12734AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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