rs12634559

Variant names:

• chr3-190870555-G-A
• rs12634559
• ENST00000479491.5:n.85-11539C>T

Variant summary

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

The ENST00000479491.5(GMNC):​n.85-11539C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,988 control chromosomes in the GnomAD database, including 20,712 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 0.47 (20712 hom., cov: 32)
• Consequence: GMNC ENST00000479491.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

GMNC (HGNC:40049): (geminin coiled-coil domain containing) Predicted to enable chromatin binding activity. Predicted to be involved in DNA replication; negative regulation of DNA replication; and negative regulation of cell cycle. Predicted to act upstream of or within cilium assembly. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GMNC	ENST00000479491.5	n.85-11539C>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72071 AN: 151870 Hom.: 20660 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.475 AC: 72179 AN: 151988 Hom.: 20712 Cov.: 32 AF XY: 0.479 AC XY: 35588 AN XY: 74308

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.452

Alfa AF: 0.347 Hom.: 14146

Bravo AF: 0.500

Asia WGS AF: 0.555 AC: 1932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12634559; hg19: chr3-190588344;