dbSNP rs1374284: POLR2DP1:n.112996006C>G (chr2-112996006-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

POLR2DP1
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

Publications

2 publications found

Variant links:

Genes affected

POLR2DP1 (HGNC:54764): (POLR2D pseudogene 1)

POLR2DP1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR2DP1		n.112996006C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR2DP1	ENST00000453215.2 link	n.*69C>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

401712

Hom.:

AF XY:

0.00

AC XY:

AN XY:

212848

African (AFR)

AF:

0.00

AC:

AN:

10442

American (AMR)

AF:

0.00

AC:

AN:

17094

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11286

East Asian (EAS)

AF:

0.00

AC:

AN:

27266

South Asian (SAS)

AF:

0.00

AC:

AN:

34446

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42460

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1828

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

234618

Other (OTH)

AF:

0.00

AC:

AN:

22272

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.9

(source)

DANN

Benign

0.53

PhyloP100

-0.18

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over