rs3758549

Positions:

• chr10-102244438-G-A

Variant summary

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

The NM_001391923.1(GBF1):​c.-11+13522G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,138 control chromosomes in the GnomAD database, including 1,895 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 0.14 (1895 hom., cov: 32)
• Consequence: GBF1 NM_001391923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

GBF1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GBF1	NM_001391923.1	c.-11+13522G>A		intron_variant
GBF1	NM_001391924.1	c.-148-1206G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21798 AN: 152022 Hom.: 1899 Cov.: 32

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0880

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.143 AC: 21799 AN: 152138 Hom.: 1895 Cov.: 32 AF XY: 0.143 AC XY: 10618 AN XY: 74370

Gnomad4 AFR AF: 0.0487

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0868

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.152

Alfa AF: 0.184 Hom.: 3736

Bravo AF: 0.133

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758549; hg19: chr10-104004195;