rs9285101

Positions:

• chr13-33913078-C-A
• chr13-33913078-C-T

Variant summary

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

The XM_017020680.3(RFC3):​c.*23889C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,100 control chromosomes in the GnomAD database, including 522 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 0.067 (522 hom., cov: 32)
• Consequence: RFC3 XM_017020680.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

RFC3 (HGNC:9971): (replication factor C subunit 3) The elongation of primed DNA templates by DNA polymerase delta and DNA polymerase epsilon requires the accessory proteins proliferating cell nuclear antigen (PCNA) and replication factor C (RFC). RFC, also named activator 1, is a protein complex consisting of five distinct subunits of 140, 40, 38, 37, and 36 kDa. This gene encodes the 38 kDa subunit. This subunit is essential for the interaction between the 140 kDa subunit and the core complex that consists of the 36, 37, and 40 kDa subunits. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

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 = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RFC3	XM_017020680.3	c.*23889C>A		3_prime_UTR_variant	9/9		XP_016876169.1
RFC3	XM_047430489.1	c.*22039C>A		3_prime_UTR_variant	10/10		XP_047286445.1
RFC3	XM_047430490.1	c.*5154C>A		3_prime_UTR_variant	10/10		XP_047286446.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RFC3	ENST00000434425.5	c.880-53009C>A		intron_variant		5		ENSP00000401001
RFC3	ENST00000616236.1	c.274-53009C>A		intron_variant		3		ENSP00000484747

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10132 AN: 151980 Hom.: 518 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0214

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0668 AC: 10155 AN: 152100 Hom.: 522 Cov.: 32 AF XY: 0.0682 AC XY: 5070 AN XY: 74372

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0214

Gnomad4 NFE AF: 0.0264

Gnomad4 OTH AF: 0.0544

Alfa AF: 0.0289 Hom.: 33

Bravo AF: 0.0704

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9285101; hg19: chr13-34487215;