17-1874133-A-G

Position:

• chr17-1874133-A-G

Variant summary

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

The NM_002945.5(RPA1):​c.455-1528A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,256 control chromosomes in the GnomAD database, including 3,234 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 0.20 (3234 hom., cov: 30)
• Consequence: RPA1 NM_002945.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

RPA1 (HGNC:10289): (replication protein A1) This gene encodes the largest subunit of the heterotrimeric Replication Protein A (RPA) complex, which binds to single-stranded DNA (ssDNA), forming a nucleoprotein complex that plays an important role in DNA metabolism, being involved in DNA replication, repair, recombination, telomere maintenance, and co-ordinating the cellular response to DNA damage through activation of the ataxia telangiectasia and Rad3-related protein (ATR) kinase. The nucleoprotein complex protects the single-stranded DNA from nucleases, prevents formation of secondary structures that would interfere with repair, and co-ordinates the recruitment and departure of different genome maintenance factors. This subunit contains four oligonucleotide/oligosaccharide-binding (OB) domains, though the majority of ssDNA binding occurs in two of these domains. The heterotrimeric complex has two different modes of ssDNA binding, a low-affinity and high-affinity mode, determined by which ssDNA binding domains are utilized. The different binding modes differ in the length of DNA bound and in the proteins with which it interacts, thereby playing a role in regulating different genomic maintenance pathways. [provided by RefSeq, Sep 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPA1	NM_002945.5	c.455-1528A>G		intron_variant		ENST00000254719.10	NP_002936.1
RPA1	NM_001355120.2	c.416-1528A>G		intron_variant			NP_001342049.1
RPA1	NM_001355121.2	c.455-1528A>G		intron_variant			NP_001342050.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPA1	ENST00000254719.10	c.455-1528A>G		intron_variant		1	NM_002945.5	ENSP00000254719	P1
RPA1	ENST00000570451.5	c.416-1528A>G		intron_variant		3		ENSP00000459788
RPA1	ENST00000573924.1	n.179-1528A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29685 AN: 151140 Hom.: 3232 Cov.: 30

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.196 AC: 29705 AN: 151256 Hom.: 3234 Cov.: 30 AF XY: 0.204 AC XY: 15100 AN XY: 73856

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.195

Alfa AF: 0.179 Hom.: 1380

Bravo AF: 0.194

Asia WGS AF: 0.331 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs7501623; hg19: chr17-1777427;