chr3-179401348-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_021629.4(GNB4):c.917-29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0021 in 1,504,044 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0022 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 7 hom. )
Consequence
GNB4
NM_021629.4 intron
NM_021629.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.49
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 3-179401348-C-T is Benign according to our data. Variant chr3-179401348-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1194837.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00218 (331/152148) while in subpopulation NFE AF= 0.00234 (159/68006). AF 95% confidence interval is 0.00204. There are 2 homozygotes in gnomad4. There are 180 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 331 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNB4 | NM_021629.4 | c.917-29G>A | intron_variant | ENST00000232564.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNB4 | ENST00000232564.8 | c.917-29G>A | intron_variant | 1 | NM_021629.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00218 AC: 331AN: 152030Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00223 AC: 537AN: 240890Hom.: 2 AF XY: 0.00207 AC XY: 270AN XY: 130420
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GnomAD4 exome AF: 0.00209 AC: 2831AN: 1351896Hom.: 7 Cov.: 19 AF XY: 0.00203 AC XY: 1379AN XY: 677902
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GnomAD4 genome ? AF: 0.00218 AC: 331AN: 152148Hom.: 2 Cov.: 32 AF XY: 0.00242 AC XY: 180AN XY: 74370
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at