chr13-33913078-C-A

Variant names:

• chr13-33913078-C-A
• rs9285101
• XR_007063695.1:n.24861C>A

Variant summary

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

The XR_007063695.1(RFC3):​n.24861C>A variant causes a non coding transcript exon 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 XR_007063695.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 1 publications found

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

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 = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434425.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFC3	NM_181558.3		c.880-53009C>A		intron	N/A	NP_853536.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFC3	ENST00000434425.5	TSL:5	c.880-53009C>A		intron	N/A	ENSP00000401001.1
	RFC3	ENST00000616236.1	TSL:3	c.274-53009C>A		intron	N/A	ENSP00000484747.1

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

African (AFR) AF: 0.144 AC: 5992 AN: 41506

American (AMR) AF: 0.0527 AC: 805 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3472

East Asian (EAS) AF: 0.114 AC: 589 AN: 5154

South Asian (SAS) AF: 0.108 AC: 518 AN: 4818

European-Finnish (FIN) AF: 0.0214 AC: 227 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0264 AC: 1792 AN: 67958

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0318 Hom.: 43

Bravo AF: 0.0704

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		0.043
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9285101; hg19: chr13-34487215;