rs1789502

Variant names:

• chr18-36038869-T-C
• rs1789502
• NM_018170.5:c.152-5032A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-36038869-T-C
• chr18-36038869-T-G

Variant summary

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

The NM_018170.5(RPRD1A):​c.152-5032A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.993 in 152,310 control chromosomes in the GnomAD database, including 75,027 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 0.99 (75027 hom., cov: 31)
• Consequence: RPRD1A NM_018170.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 1 publications found

Genes affected

RPRD1A (HGNC:25560): (regulation of nuclear pre-mRNA domain containing 1A) This gene encodes a cell-cycle and transcription regulatory protein. The encoded protein interacts with the cell cycle inhibitor cyclin-dependent kinase 4 inhibitor B and may function as a negative regulator of G(1)/S phase progression. This protein also forms homo- and hetrodimers with the protein, regulation of nuclear pre-mRNA domain-containing protein 1B, to form a scaffold that interacts with the C-terminal domain of RNA polymerase II subunit B1 and regulates several aspects of transcription. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 16. [provided by RefSeq, Dec 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018170.5. 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
	RPRD1A	NM_018170.5	MANE Select	c.152-5032A>G		intron	N/A	NP_060640.2
	RPRD1A	NM_001303413.2		c.152-5032A>G		intron	N/A	NP_001290342.1
	RPRD1A	NM_001303411.2		c.43+1938A>G		intron	N/A	NP_001290340.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPRD1A	ENST00000399022.9	TSL:1 MANE Select	c.152-5032A>G		intron	N/A	ENSP00000381984.3
	RPRD1A	ENST00000590898.5	TSL:1	c.43+1938A>G		intron	N/A	ENSP00000467991.1
	RPRD1A	ENST00000589050.1	TSL:1	n.152-5032A>G		intron	N/A	ENSP00000468209.1

Frequencies

GnomAD3 genomes AF: 0.993 AC: 151053 AN: 152192 Hom.: 74969 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.995

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

GnomAD4 genome AF: 0.993 AC: 151170 AN: 152310 Hom.: 75027 Cov.: 31 AF XY: 0.993 AC XY: 73949 AN XY: 74484

African (AFR) AF: 0.975 AC: 40506 AN: 41558

American (AMR) AF: 0.996 AC: 15240 AN: 15308

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5174 AN: 5174

South Asian (SAS) AF: 1.00 AC: 4828 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10614 AN: 10614

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68031 AN: 68040

Other (OTH) AF: 0.995 AC: 2100 AN: 2110

Alfa AF: 0.996 Hom.: 4467

Bravo AF: 0.992

Asia WGS AF: 0.999 AC: 3473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		-0.63
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: rs1789502; hg19: chr18-33618832;