10-102382537-G-T

Variant names:

• chr10-102382537-G-T
• rs1057050
• NM_001377137.1:c.*201G>T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PM2 BP4_Strong BS2

The NM_001377137.1(GBF1):​c.*201G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 381,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.000013 (0 hom.)
• Consequence: GBF1 NM_001377137.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• axonal neuropathy

  Inheritance: AD Classification: STRONG Submitted by: Franklin by Genoox

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS2: High AC in GnomAdExome4 at 5 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377137.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GBF1	NM_001377137.1	MANE Select	c.*201G>T		3_prime_UTR	Exon 40 of 40	NP_001364066.1	Q92538-4
	GBF1	NM_001411027.1		c.*201G>T		3_prime_UTR	Exon 41 of 41	NP_001397956.1	A0A669KBG8
	GBF1	NM_001391922.1		c.*201G>T		3_prime_UTR	Exon 41 of 41	NP_001378851.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GBF1	ENST00000369983.5	TSL:1 MANE Select	c.*201G>T		3_prime_UTR	Exon 40 of 40	ENSP00000359000.4	Q92538-4
	GBF1	ENST00000679080.1		c.383G>T	p.Arg128Leu	missense	Exon 2 of 2	ENSP00000503258.1	A0A7I2V350
	GBF1	ENST00000673650.1		c.*201G>T		3_prime_UTR	Exon 41 of 41	ENSP00000501233.1	A0A669KBG8

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.0000131 AC: 5 AN: 381266 Hom.: 0 Cov.: 4 AF XY: 0.0000151 AC XY: 3 AN XY: 199232

African (AFR) AF: 0.00 AC: 0 AN: 10568

American (AMR) AF: 0.00 AC: 0 AN: 12384

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12366

East Asian (EAS) AF: 0.00 AC: 0 AN: 26678

South Asian (SAS) AF: 0.00 AC: 0 AN: 31150

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26936

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1788

European-Non Finnish (NFE) AF: 0.0000169 AC: 4 AN: 236580

Other (OTH) AF: 0.0000438 AC: 1 AN: 22816

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.54
PhyloP100		-0.22
PromoterAI		0.0080	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs1057050; hg19: chr10-104142294;