rs9682599

Variant names:

• chr3-190863372-T-C
• rs9682599
• ENST00000479491.5:n.85-4356A>G

Variant summary

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

The ENST00000479491.5(GMNC):​n.85-4356A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GMNC	ENST00000479491.5	n.85-4356A>G		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.268 AC: 11100 AN: 41446

American (AMR) AF: 0.104 AC: 1588 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0878 AC: 305 AN: 3472

East Asian (EAS) AF: 0.0923 AC: 478 AN: 5176

South Asian (SAS) AF: 0.176 AC: 847 AN: 4816

European-Finnish (FIN) AF: 0.0961 AC: 1017 AN: 10578

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9528 AN: 67988

Other (OTH) AF: 0.151 AC: 319 AN: 2116

Alfa AF: 0.146 Hom.: 3264

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
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs9682599; hg19: chr3-190581161;