Genetic Variant GLIPR1:c.*3906C>T (chr12-75502884-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006851.3(GLIPR1):c.*3906C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,922 control chromosomes in the GnomAD database, including 4,448 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 0.24 ( 4448 hom., cov: 32)

Exomes 𝑓: 0.067 ( 0 hom. )

Consequence

GLIPR1
NM_006851.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0570

Variant links:

Genes affected

GLIPR1 (HGNC:17001): (GLI pathogenesis related 1) This gene encodes a protein with similarity to both the pathogenesis-related protein (PR) superfamily and the cysteine-rich secretory protein (CRISP) family. Increased expression of this gene is associated with myelomocytic differentiation in macrophage and decreased expression of this gene through gene methylation is associated with prostate cancer. The protein has proapoptotic activities in prostate and bladder cancer cells. This gene is a member of a cluster on chromosome 12 containing two other similar genes. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

GLIPR1 links:

KRR1 (HGNC:5176): (KRR1 small subunit processome component homolog) Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in chromosome; intercellular bridge; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

KRR1 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GLIPR1	NM_006851.3 link	c.*3906C>T	3_prime_UTR_variant	Exon 6 of 6	ENST00000266659.8	NP_006842.2	P48060-1
KRR1	NM_007043.7 link	c.832-884G>A	intron_variant	Intron 7 of 9	ENST00000229214.9	NP_008974.5	Q13601-1
KRR1	XM_047428133.1 link	c.538-884G>A	intron_variant	Intron 7 of 9		XP_047284089.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GLIPR1	ENST00000266659.8 link	c.*3906C>T	3_prime_UTR_variant	Exon 6 of 6	1	NM_006851.3	ENSP00000266659.3	P48060-1
KRR1	ENST00000229214.9 link	c.832-884G>A	intron_variant	Intron 7 of 9	1	NM_007043.7	ENSP00000229214.4	Q13601-1
KRR1	ENST00000438169.6 link	c.661-884G>A	intron_variant	Intron 6 of 8	1		ENSP00000411740.2	Q13601-2
KRR1	ENST00000551070.5 link	n.380-884G>A	intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35683

AN:

151772

Hom.:

4440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.100

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.317

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.325

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.268

GnomAD4 exome

AF:

0.0667

AC:

AN:

Hom.:

Cov.:

AF XY:

0.111

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AC:

AN:

Gnomad4 AMR exome

AC:

AN:

Gnomad4 ASJ exome

AC:

AN:

Gnomad4 EAS exome

AC:

AN:

Gnomad4 SAS exome

AC:

AN:

Gnomad4 FIN exome

AF:

0.0833

AC:

AN:

Gnomad4 NFE exome

AF:

0.00

AC:

AN:

Gnomad4 Remaining exome

AC:

AN:

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.235

AC:

35710

AN:

151892

Hom.:

4448

Cov.:

AF XY:

0.234

AC XY:

17406

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.208

AC:

0.207624

AN:

0.207624

Gnomad4 AMR

AF:

0.293

AC:

0.292592

AN:

0.292592

Gnomad4 ASJ

AF:

0.246

AC:

0.245675

AN:

0.245675

Gnomad4 EAS

AF:

0.118

AC:

0.118421

AN:

0.118421

Gnomad4 SAS

AF:

0.317

AC:

0.31722

AN:

0.31722

Gnomad4 FIN

AF:

0.192

AC:

0.192221

AN:

0.192221

Gnomad4 NFE

AF:

0.249

AC:

0.248607

AN:

0.248607

Gnomad4 OTH

AF:

0.268

AC:

0.268281

AN:

0.268281

Heterozygous variant carriers

1386

2771

4157

5542

6928

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

376

752

1128

1504

1880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.261

Hom.:

915

Bravo

AF:

0.239

Asia WGS

AF:

0.219

AC:

761

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

1.5

DANN

Benign

0.59

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over