Variant 7-102476231-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_006234.6(POLR2J):c.93T>C(p.Cys31Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 0 hom., cov: 15)

Exomes 𝑓: 0.00069 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

POLR2J
NM_006234.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.471

Variant links:

Genes affected

POLR2J (HGNC:9197): (RNA polymerase II subunit J) This gene encodes a subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. The product of this gene exists as a heterodimer with another polymerase subunit; together they form a core subassembly unit of the polymerase. Two similar genes are located nearby on chromosome 7q22.1 and a pseudogene is found on chromosome 7p13. [provided by RefSeq, Jul 2008]

POLR2J links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 7-102476231-A-G is Benign according to our data. Variant chr7-102476231-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2657885.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.471 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR2J	NM_006234.6 link	c.93T>C	p.Cys31Cys	synonymous_variant	2/4	ENST00000292614.10	NP_006225.1	P52435

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR2J	ENST00000292614.10 link	c.93T>C	p.Cys31Cys	synonymous_variant	2/4	1	NM_006234.6	ENSP00000292614.5		P52435

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

331

AN:

124350

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00718

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00156

Gnomad ASJ

AF:

0.00594

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000559

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0110

Gnomad NFE

AF:

0.000606

Gnomad OTH

AF:

0.00379

GnomAD3 exomes

AF:

0.00117

AC:

144

AN:

122690

Hom.:

AF XY:

0.00122

AC XY:

AN XY:

65718

show subpopulations

Gnomad AFR exome

AF:

0.00429

Gnomad AMR exome

AF:

0.00139

Gnomad ASJ exome

AF:

0.00475

Gnomad EAS exome

AF:

0.000458

Gnomad SAS exome

AF:

0.00140

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000490

Gnomad OTH exome

AF:

0.00158

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000688

AC:

524

AN:

761946

Hom.:

Cov.:

AF XY:

0.000798

AC XY:

317

AN XY:

397294

show subpopulations

Gnomad4 AFR exome

AF:

0.00229

Gnomad4 AMR exome

AF:

0.000858

Gnomad4 ASJ exome

AF:

0.00614

Gnomad4 EAS exome

AF:

0.000142

Gnomad4 SAS exome

AF:

0.00110

Gnomad4 FIN exome

AF:

0.0000837

Gnomad4 NFE exome

AF:

0.000378

Gnomad4 OTH exome

AF:

0.00144

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00264

AC:

329

AN:

124476

Hom.:

Cov.:

AF XY:

0.00249

AC XY:

149

AN XY:

59768

show subpopulations

Gnomad4 AFR

AF:

0.00712

Gnomad4 AMR

AF:

0.00156

Gnomad4 ASJ

AF:

0.00594

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000559

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000606

Gnomad4 OTH

AF:

0.00374

Alfa

AF:

0.00290

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

POLR2J: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

8.8

DANN

Benign

0.75

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over