rs909859

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-38109720-G-C
• chr20-38109720-G-T

Variant summary

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

The ENST00000614670.1(RPRD1B):​c.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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPRD1B	ENST00000614670.1	c.175-17577G>C		intron_variant	Intron 1 of 1	3		ENSP00000484897.1
RPRD1B	ENST00000618318.1	n.256-15050G>C		intron_variant	Intron 2 of 2	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;