10-102245629-G-A

Position:

• chr10-102245629-G-A

Variant summary

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

The NM_001377137.1(GBF1):​c.-163G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,116 control chromosomes in the GnomAD database, including 33,352 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 0.66 (33347 hom., cov: 32)
  • Exomes 𝑓: 0.57 (5 hom.)
• Consequence: GBF1 NM_001377137.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

GBF1 (HGNC:4181): (golgi brefeldin A resistant guanine nucleotide exchange factor 1) This gene encodes a member of the Sec7 domain family. The encoded protein is a guanine nucleotide exchange factor that regulates the recruitment of proteins to membranes by mediating GDP to GTP exchange. The encoded protein is localized to the Golgi apparatus and plays a role in vesicular trafficking by activating ADP ribosylation factor 1. The encoded protein has also been identified as an important host factor for viral replication. Multiple transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]

GBF1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GBF1	NM_001377137.1	c.-163G>A		5_prime_UTR_variant	1/40	ENST00000369983.5	NP_001364066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GBF1	ENST00000369983	c.-163G>A		5_prime_UTR_variant	1/40	1	NM_001377137.1	ENSP00000359000.4

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99995 AN: 151956 Hom.: 33292 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.628

GnomAD4 exome AF: 0.571 AC: 24 AN: 42 Hom.: 5 Cov.: 0 AF XY: 0.611 AC XY: 22 AN XY: 36

Gnomad4 AFR exome AF: 0.750

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.583

GnomAD4 genome AF: 0.658 AC: 100109 AN: 152074 Hom.: 33347 Cov.: 32 AF XY: 0.655 AC XY: 48707 AN XY: 74342

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.633

Alfa AF: 0.618 Hom.: 37845

Bravo AF: 0.663

Asia WGS AF: 0.638 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.71
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1541046; hg19: chr10-104005386;