rs754574

chr3-179460067-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047448653.1(GNB4):c.-42-33825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,136 control chromosomes in the GnomAD database, including 8,575 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8575 hom., cov: 33)
• Consequence: GNB4 XM_047448653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524

Genes affected

GNB4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNB4	XM_047448653.1	c.-42-33825G>A		intron_variant
GNB4	XM_047448654.1	c.-42-33825G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49333 AN: 152020 Hom.: 8567 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.313

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.325 AC: 49370 AN: 152136 Hom.: 8575 Cov.: 33 AF XY: 0.322 AC XY: 23991 AN XY: 74394

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.309

Alfa AF: 0.310 Hom.: 2063

Bravo AF: 0.328

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.5
Dann	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs754574; hg19: chr3-179177855;