chr20-38060491-A-G

Variant names:

• chr20-38060491-A-G
• rs6022716
• NM_021215.4:c.655+971A>G

Variant summary

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

The NM_021215.4(RPRD1B):​c.655+971A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,058 control chromosomes in the GnomAD database, including 28,559 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 0.58 (28559 hom., cov: 32)
• Consequence: RPRD1B NM_021215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021215.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPRD1B	NM_021215.4	MANE Select	c.655+971A>G		intron	N/A	NP_067038.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPRD1B	ENST00000373433.9	TSL:1 MANE Select	c.655+971A>G		intron	N/A	ENSP00000362532.4
	RPRD1B	ENST00000881436.1		c.655+971A>G		intron	N/A	ENSP00000551495.1
	RPRD1B	ENST00000881433.1		c.649+971A>G		intron	N/A	ENSP00000551492.1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88713 AN: 151940 Hom.: 28510 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.584 AC: 88822 AN: 152058 Hom.: 28559 Cov.: 32 AF XY: 0.581 AC XY: 43161 AN XY: 74316

African (AFR) AF: 0.871 AC: 36141 AN: 41484

American (AMR) AF: 0.438 AC: 6693 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3470

East Asian (EAS) AF: 0.608 AC: 3142 AN: 5164

South Asian (SAS) AF: 0.602 AC: 2907 AN: 4826

European-Finnish (FIN) AF: 0.412 AC: 4341 AN: 10548

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32133 AN: 67978

Other (OTH) AF: 0.575 AC: 1215 AN: 2112

Alfa AF: 0.531 Hom.: 4069

Bravo AF: 0.592

Asia WGS AF: 0.623 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		0.31
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: rs6022716; hg19: chr20-36688893;