3-179401278-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_021629.4(GNB4):c.958G>A(p.Val320Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00308 in 1,613,740 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V320L) has been classified as Uncertain significance.
Frequency
Consequence
NM_021629.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNB4 | NM_021629.4 | c.958G>A | p.Val320Ile | missense_variant | 10/10 | ENST00000232564.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNB4 | ENST00000232564.8 | c.958G>A | p.Val320Ile | missense_variant | 10/10 | 1 | NM_021629.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00341 AC: 518AN: 152042Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00419 AC: 1053AN: 251200Hom.: 8 AF XY: 0.00407 AC XY: 553AN XY: 135770
GnomAD4 exome AF: 0.00305 AC: 4455AN: 1461580Hom.: 26 Cov.: 30 AF XY: 0.00306 AC XY: 2222AN XY: 727082
GnomAD4 genome AF: 0.00340 AC: 518AN: 152160Hom.: 4 Cov.: 33 AF XY: 0.00406 AC XY: 302AN XY: 74390
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 13, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | GNB4: BS1, BS2 - |
Charcot-Marie-Tooth disease dominant intermediate F Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 23, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at