rs2754775

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015895.5(GMNN):​c.-317G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,322 control chromosomes in the GnomAD database, including 2,010 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 0.15 ( 2010 hom., cov: 33)
Exomes 𝑓: 0.12 ( 0 hom. )

Consequence

GMNN
NM_015895.5 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.497
Variant links:
Genes affected
GMNN (HGNC:17493): (geminin DNA replication inhibitor) This gene encodes a protein that plays a critical role in cell cycle regulation. The encoded protein inhibits DNA replication by binding to DNA replication factor Cdt1, preventing the incorporation of minichromosome maintenance proteins into the pre-replication complex. The encoded protein is expressed during the S and G2 phases of the cell cycle and is degraded by the anaphase-promoting complex during the metaphase-anaphase transition. Increased expression of this gene may play a role in several malignancies including colon, rectal and breast cancer. Alternatively spliced transcript variants have been observed for this gene, and two pseudogenes of this gene are located on the short arm of chromosome 16. [provided by RefSeq, Oct 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GMNNNM_015895.5 linkuse as main transcriptc.-317G>T 5_prime_UTR_variant 1/7 ENST00000230056.8
GMNNNM_001251989.2 linkuse as main transcriptc.-185G>T 5_prime_UTR_variant 1/7
GMNNNM_001251990.2 linkuse as main transcriptc.-109G>T 5_prime_UTR_variant 1/7
GMNNXM_005249159.3 linkuse as main transcriptc.-897G>T 5_prime_UTR_variant 1/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GMNNENST00000230056.8 linkuse as main transcriptc.-317G>T 5_prime_UTR_variant 1/71 NM_015895.5 P1
GMNNENST00000356509.7 linkuse as main transcriptc.-185G>T 5_prime_UTR_variant 1/72 P1
GMNNENST00000468943.1 linkuse as main transcriptn.5G>T non_coding_transcript_exon_variant 1/22

Frequencies

GnomAD3 genomes
AF:
0.153
AC:
23269
AN:
152146
Hom.:
2008
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.229
Gnomad AMI
AF:
0.196
Gnomad AMR
AF:
0.146
Gnomad ASJ
AF:
0.187
Gnomad EAS
AF:
0.108
Gnomad SAS
AF:
0.255
Gnomad FIN
AF:
0.0828
Gnomad MID
AF:
0.212
Gnomad NFE
AF:
0.111
Gnomad OTH
AF:
0.185
GnomAD4 exome
AF:
0.121
AC:
7
AN:
58
Hom.:
0
Cov.:
0
AF XY:
0.140
AC XY:
7
AN XY:
50
show subpopulations
Gnomad4 AFR exome
AF:
0.250
Gnomad4 FIN exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.0625
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.153
AC:
23294
AN:
152264
Hom.:
2010
Cov.:
33
AF XY:
0.153
AC XY:
11361
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.229
Gnomad4 AMR
AF:
0.146
Gnomad4 ASJ
AF:
0.187
Gnomad4 EAS
AF:
0.109
Gnomad4 SAS
AF:
0.254
Gnomad4 FIN
AF:
0.0828
Gnomad4 NFE
AF:
0.111
Gnomad4 OTH
AF:
0.184
Alfa
AF:
0.125
Hom.:
531
Bravo
AF:
0.159
Asia WGS
AF:
0.226
AC:
785
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
6.1
DANN
Benign
0.70

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.

Other links and lift over

dbSNP: rs2754775; hg19: chr6-24775181; API