rs3783197

Variant names:

• chr13-41469534-G-A
• rs3783197
• NM_014059.3:c.406+696G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-41469534-G-A
• chr13-41469534-G-T

Variant summary

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

The NM_014059.3(RGCC):​c.406+696G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,938 control chromosomes in the GnomAD database, including 14,336 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 0.40 (14336 hom., cov: 30)
• Consequence: RGCC NM_014059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 8 publications found

Genes affected

RGCC (HGNC:20369): (regulator of cell cycle) This gene is thought to regulate cell cycle progression. It is induced by p53 in response to DNA damage, or by sublytic levels of complement system proteins that result in activation of the cell cycle. The encoded protein localizes to the cytoplasm during interphase and to centrosomes during mitosis. The protein forms a complex with polo-like kinase 1. The protein also translocates to the nucleus in response to treatment with complement system proteins, and can associate with and increase the kinase activity of cell division cycle 2 protein. In different assays and cell types, overexpression of this protein has been shown to activate or suppress cell cycle progression. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGCC	NM_014059.3	c.406+696G>A		intron_variant	Intron 4 of 4	ENST00000379359.4	NP_054778.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGCC	ENST00000379359.4	c.406+696G>A		intron_variant	Intron 4 of 4	1	NM_014059.3	ENSP00000368664.3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61343 AN: 151820 Hom.: 14332 Cov.: 30

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.404 AC: 61356 AN: 151938 Hom.: 14336 Cov.: 30 AF XY: 0.413 AC XY: 30686 AN XY: 74242

African (AFR) AF: 0.151 AC: 6274 AN: 41484

American (AMR) AF: 0.417 AC: 6372 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1820 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1949 AN: 5148

South Asian (SAS) AF: 0.650 AC: 3130 AN: 4812

European-Finnish (FIN) AF: 0.562 AC: 5901 AN: 10498

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34308 AN: 67948

Other (OTH) AF: 0.417 AC: 880 AN: 2110

Alfa AF: 0.472 Hom.: 78204

Bravo AF: 0.376

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.34
DANN	Benign	0.68
PhyloP100		-0.66
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

Other links and lift over

dbSNP: rs3783197; hg19: chr13-42043670;