rs909859

chr20-38109720-G-Cchr20-38109720-G-T

Variant summary

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

The ENST00000614670.1(RPRD1B):c.176-17577G>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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPRD1B	ENST00000614670.1	c.176-17577G>C		intron_variant		3
RPRD1B	ENST00000618318.1	n.256-15050G>C		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.581

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.19
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs909859; hg19: chr20-36738122;