7-102473462-C-A

Variant names:

• chr7-102473462-C-A
• rs1131383
• NM_006234.6:c.*187G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006234.6(POLR2J):​c.*187G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: POLR2J NM_006234.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 31 publications found

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]

ACMG classification

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=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR2J	NM_006234.6	c.*187G>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000292614.10	NP_006225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR2J	ENST00000292614.10	c.*187G>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_006234.6	ENSP00000292614.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 650278 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 327772

African (AFR) AF: 0.00 AC: 0 AN: 14446

American (AMR) AF: 0.00 AC: 0 AN: 15554

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14092

East Asian (EAS) AF: 0.00 AC: 0 AN: 29014

South Asian (SAS) AF: 0.00 AC: 0 AN: 38988

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27872

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2370

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 476478

Other (OTH) AF: 0.00 AC: 0 AN: 31464

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 129915

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.73
PhyloP100		0.015

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: rs1131383; hg19: chr7-102113909;