rs6023059

Variant names:

• chr20-38109369-T-C
• rs6023059
• ENST00000614670.1:c.175-17928T>C

Variant summary

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

The ENST00000614670.1(RPRD1B):​c.175-17928T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,138 control chromosomes in the GnomAD database, including 28,982 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 (28982 hom., cov: 32)
• Consequence: RPRD1B ENST00000614670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPRD1B	ENST00000614670.1	c.175-17928T>C		intron_variant	Intron 1 of 1	3		ENSP00000484897.1
RPRD1B	ENST00000618318.1	n.256-15401T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89147 AN: 152020 Hom.: 28933 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.587 AC: 89255 AN: 152138 Hom.: 28982 Cov.: 32 AF XY: 0.583 AC XY: 43315 AN XY: 74356

African (AFR) AF: 0.883 AC: 36699 AN: 41550

American (AMR) AF: 0.439 AC: 6717 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1702 AN: 3472

East Asian (EAS) AF: 0.607 AC: 3135 AN: 5166

South Asian (SAS) AF: 0.599 AC: 2887 AN: 4820

European-Finnish (FIN) AF: 0.405 AC: 4283 AN: 10572

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32040 AN: 67958

Other (OTH) AF: 0.582 AC: 1229 AN: 2112

Alfa AF: 0.535 Hom.: 3869

Bravo AF: 0.595

Asia WGS AF: 0.622 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.75
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs6023059; hg19: chr20-36737771;