rs9682599

Positions:

• chr3-190863372-T-C

Variant summary

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

The ENST00000479491.5(GMNC):​n.85-4356A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,084 control chromosomes in the GnomAD database, including 2,387 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 0.17 (2387 hom., cov: 32)
• Consequence: GMNC ENST00000479491.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GMNC	ENST00000479491.5	n.85-4356A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25252 AN: 151966 Hom.: 2385 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.166 AC: 25287 AN: 152084 Hom.: 2387 Cov.: 32 AF XY: 0.163 AC XY: 12123 AN XY: 74370

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.151

Alfa AF: 0.143 Hom.: 2222

Bravo AF: 0.170

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9682599; hg19: chr3-190581161;