rs7902537

chr10-102282852-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.163+22736G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0545 in 152,222 control chromosomes in the GnomAD database, including 479 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 0.054 (479 hom., cov: 32)
• Consequence: GBF1 NM_001377137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GBF1	NM_001377137.1	c.163+22736G>A		intron_variant		ENST00000369983.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GBF1	ENST00000369983.5	c.163+22736G>A		intron_variant		1	NM_001377137.1	P4

Frequencies

GnomAD3 genomes AF: 0.0544 AC: 8268 AN: 152104 Hom.: 477 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0355

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0545 AC: 8295 AN: 152222 Hom.: 479 Cov.: 32 AF XY: 0.0521 AC XY: 3880 AN XY: 74450

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0355

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.00264

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0402 Hom.: 41

Bravo AF: 0.0603

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.3
Dann	Benign	0.19

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: rs7902537; hg19: chr10-104042609;