rs1329119

Positions:

• chr1-89108343-G-A
• chr1-89108343-G-C
• chr1-89108343-G-T

Variant summary

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

The NM_004120.5(GBP2):​c.1660-52C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 1,136,592 control chromosomes in the GnomAD database, including 286,483 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 0.74 (41701 hom., cov: 32)
  • Exomes 𝑓: 0.70 (244782 hom.)
• Consequence: GBP2 NM_004120.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

GBP2 (HGNC:4183): (guanylate binding protein 2) This gene belongs to the guanine-binding protein (GBP) family, which includes interferon-induced proteins that can bind to guanine nucleotides (GMP, GDP and GTP). The encoded protein is a GTPase which hydrolyzes GTP, predominantly to GDP. The protein may play a role as a marker of squamous cell carcinomas. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GBP2	NM_004120.5	c.1660-52C>T		intron_variant		ENST00000370466.4	NP_004111.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GBP2	ENST00000370466.4	c.1660-52C>T		intron_variant		1	NM_004120.5	ENSP00000359497	P1
GBP2	ENST00000464839.5	c.1660-52C>T		intron_variant, NMD_transcript_variant		2		ENSP00000434282
GBP2	ENST00000493802.5	n.620-52C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112161 AN: 152070 Hom.: 41653 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.715

GnomAD3 exomes AF: 0.721 AC: 159690 AN: 221496 Hom.: 58032 AF XY: 0.714 AC XY: 85730 AN XY: 120100

Gnomad AFR exome AF: 0.815

Gnomad AMR exome AF: 0.750

Gnomad ASJ exome AF: 0.630

Gnomad EAS exome AF: 0.793

Gnomad SAS exome AF: 0.693

Gnomad FIN exome AF: 0.803

Gnomad NFE exome AF: 0.687

Gnomad OTH exome AF: 0.693

GnomAD4 exome AF: 0.704 AC: 692868 AN: 984404 Hom.: 244782 Cov.: 13 AF XY: 0.703 AC XY: 358240 AN XY: 509648

Gnomad4 AFR exome AF: 0.820

Gnomad4 AMR exome AF: 0.744

Gnomad4 ASJ exome AF: 0.635

Gnomad4 EAS exome AF: 0.781

Gnomad4 SAS exome AF: 0.696

Gnomad4 FIN exome AF: 0.795

Gnomad4 NFE exome AF: 0.690

Gnomad4 OTH exome AF: 0.700

GnomAD4 genome AF: 0.738 AC: 112265 AN: 152188 Hom.: 41701 Cov.: 32 AF XY: 0.740 AC XY: 55047 AN XY: 74392

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.717

Alfa AF: 0.683 Hom.: 16039

Bravo AF: 0.732

Asia WGS AF: 0.755 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.60

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: rs1329119; hg19: chr1-89574026;