chr20-38109720-G-C

Variant names:

• chr20-38109720-G-C
• rs909859
• ENST00000614670.1:c.175-17577G>C

Variant summary

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

The ENST00000614670.1(RPRD1B):​c.175-17577G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,994 control chromosomes in the GnomAD database, including 28,933 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 0.59 (28933 hom., cov: 30)
• Consequence: RPRD1B ENST00000614670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 4 publications found

Genes affected

RPRD1B (HGNC:16209): (regulation of nuclear pre-mRNA domain containing 1B) Enables RNA polymerase II complex binding activity and identical protein binding activity. Involved in positive regulation of cell population proliferation; regulation of cell cycle process; and regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of RNA polymerase II, holoenzyme. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614670.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPRD1B	ENST00000614670.1	TSL:3	c.175-17577G>C		intron	N/A	ENSP00000484897.1
	RPRD1B	ENST00000618318.1	TSL:4	n.256-15050G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89033 AN: 151876 Hom.: 28884 Cov.: 30

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.586 AC: 89141 AN: 151994 Hom.: 28933 Cov.: 30 AF XY: 0.583 AC XY: 43282 AN XY: 74302

African (AFR) AF: 0.883 AC: 36638 AN: 41484

American (AMR) AF: 0.440 AC: 6706 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3464

East Asian (EAS) AF: 0.609 AC: 3148 AN: 5172

South Asian (SAS) AF: 0.600 AC: 2886 AN: 4810

European-Finnish (FIN) AF: 0.405 AC: 4273 AN: 10562

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 32004 AN: 67934

Other (OTH) AF: 0.581 AC: 1224 AN: 2106

Alfa AF: 0.543 Hom.: 2992

Bravo AF: 0.595

Asia WGS AF: 0.617 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.41
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs909859; hg19: chr20-36738122;