1-89065709-C-T

Variant names:

• chr1-89065709-C-T
• rs1536670
• ENST00000872735.1:c.-19-2456G>A

Variant summary

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

The ENST00000872735.1(GBP1):​c.-19-2456G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,162 control chromosomes in the GnomAD database, including 45,183 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 0.77 (45183 hom., cov: 32)
• Consequence: GBP1 ENST00000872735.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 3 publications found

Genes affected

GBP1 (HGNC:4182): (guanylate binding protein 1) Guanylate binding protein expression is induced by interferon. Guanylate binding proteins are characterized by their ability to specifically bind guanine nucleotides (GMP, GDP, and GTP) and are distinguished from the GTP-binding proteins by the presence of 2 binding motifs rather than 3. [provided by RefSeq, Jul 2008]

ENSG00000307222 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000872735.1. 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
	GBP1	ENST00000872735.1		c.-19-2456G>A		intron	N/A	ENSP00000542794.1
	ENSG00000307222	ENST00000824610.1		n.178-2116C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116813 AN: 152044 Hom.: 45140 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.768 AC: 116909 AN: 152162 Hom.: 45183 Cov.: 32 AF XY: 0.765 AC XY: 56911 AN XY: 74394

African (AFR) AF: 0.805 AC: 33398 AN: 41502

American (AMR) AF: 0.653 AC: 9986 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2908 AN: 5180

South Asian (SAS) AF: 0.780 AC: 3769 AN: 4830

European-Finnish (FIN) AF: 0.758 AC: 8021 AN: 10580

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53565 AN: 67996

Other (OTH) AF: 0.768 AC: 1620 AN: 2110

Alfa AF: 0.734 Hom.: 2571

Bravo AF: 0.760

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		-1.2
PromoterAI		-0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1536670; hg19: chr1-89531392;