chr1-89052437-A-G

Variant names:

• chr1-89052437-A-G
• rs7911
• NM_002053.3:c.*918T>C

Variant summary

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

The NM_002053.3(GBP1):​c.*918T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,960 control chromosomes in the GnomAD database, including 11,595 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 0.39 (11595 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: GBP1 NM_002053.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 25 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GBP1	NM_002053.3	c.*918T>C		3_prime_UTR_variant	Exon 11 of 11	ENST00000370473.5	NP_002044.2
LOC105378841	XR_947575.3	n.3207+5517A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GBP1	ENST00000370473.5	c.*918T>C		3_prime_UTR_variant	Exon 11 of 11	1	NM_002053.3	ENSP00000359504.4

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58520 AN: 151842 Hom.: 11577 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.399

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.386 AC: 58584 AN: 151960 Hom.: 11595 Cov.: 32 AF XY: 0.378 AC XY: 28068 AN XY: 74278

African (AFR) AF: 0.465 AC: 19252 AN: 41406

American (AMR) AF: 0.376 AC: 5745 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1286 AN: 5184

South Asian (SAS) AF: 0.357 AC: 1721 AN: 4826

European-Finnish (FIN) AF: 0.233 AC: 2462 AN: 10560

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25191 AN: 67924

Other (OTH) AF: 0.404 AC: 852 AN: 2110

Alfa AF: 0.380 Hom.: 8075

Bravo AF: 0.402

Asia WGS AF: 0.357 AC: 1240 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.88
PhyloP100		0.030
Mutation Taster		=100/0	polymorphism (auto)

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: rs7911; hg19: chr1-89518120;