rs1390669

Variant names:

• chr5-21631495-A-G
• rs1390669
• ENST00000522350.1:n.476+7385A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522350.1(GUSBP1):​n.476+7385A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0823 in 152,196 control chromosomes in the GnomAD database, including 588 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 0.082 (588 hom., cov: 33)
• Consequence: GUSBP1 ENST00000522350.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 2 publications found

Genes affected

GUSBP1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522350.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GUSBP1	ENST00000522350.1	TSL:1	n.476+7385A>G		intron	N/A
	GUSBP1	ENST00000716643.1		n.500-5579A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12505 AN: 152078 Hom.: 589 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.00655

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0741

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0823 AC: 12519 AN: 152196 Hom.: 588 Cov.: 33 AF XY: 0.0798 AC XY: 5942 AN XY: 74434

African (AFR) AF: 0.122 AC: 5068 AN: 41524

American (AMR) AF: 0.0698 AC: 1067 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3468

East Asian (EAS) AF: 0.00656 AC: 34 AN: 5182

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4822

European-Finnish (FIN) AF: 0.0545 AC: 579 AN: 10620

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0741 AC: 5041 AN: 67986

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

Alfa AF: 0.0750 Hom.: 246

Bravo AF: 0.0841

Asia WGS AF: 0.0310 AC: 107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.56
PhyloP100		0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1390669;

hg19: chr5-21631604;