rs9263733

Variant names:

• chr6-31141052-C-T
• rs9263733
• ENST00000444785.1:n.*139C>T

Variant summary

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

The ENST00000444785.1(POLR2LP1):​n.*139C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 152,178 control chromosomes in the GnomAD database, including 129 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 0.035 (129 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: POLR2LP1 ENST00000444785.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 13 publications found

Genes affected

POLR2LP1 (HGNC:31340): (RNA polymerase II subunit L pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0605 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
POLR2LP1	ENST00000444785.1	n.*139C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5344 AN: 152060 Hom.: 126 Cov.: 30

Gnomad AFR AF: 0.0475

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0364

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0662

Gnomad SAS AF: 0.0440

Gnomad FIN AF: 0.00547

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0291

Gnomad OTH AF: 0.0576

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 124 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 82

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64

Other (OTH) AF: 0.00 AC: 0 AN: 12

GnomAD4 genome AF: 0.0352 AC: 5356 AN: 152178 Hom.: 129 Cov.: 30 AF XY: 0.0349 AC XY: 2599 AN XY: 74410

African (AFR) AF: 0.0476 AC: 1975 AN: 41510

American (AMR) AF: 0.0364 AC: 556 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3468

East Asian (EAS) AF: 0.0663 AC: 343 AN: 5172

South Asian (SAS) AF: 0.0444 AC: 214 AN: 4818

European-Finnish (FIN) AF: 0.00547 AC: 58 AN: 10610

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0291 AC: 1979 AN: 68010

Other (OTH) AF: 0.0570 AC: 120 AN: 2106

Alfa AF: 0.0336 Hom.: 325

Bravo AF: 0.0389

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs9263733; hg19: chr6-31108829;