9-37482336-C-T

Variant names:

• chr9-37482336-C-T
• rs7033474
• ENST00000916168.1:c.-10+444C>T

Variant summary

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

The ENST00000916168.1(POLR1E):​c.-10+444C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.43 (13568 hom., cov: 20)
• Consequence: POLR1E ENST00000916168.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 2 publications found

Genes affected

POLR1E (HGNC:17631): (RNA polymerase I subunit E) Predicted to enable DNA binding activity; DNA-directed 5'-3' RNA polymerase activity; and RNA polymerase I general transcription initiation factor binding activity. Involved in nucleolar large rRNA transcription by RNA polymerase I. Located in fibrillar center and nucleoplasm. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000916168.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1E	ENST00000916168.1		c.-10+444C>T		intron	N/A	ENSP00000586227.1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 61847 AN: 143336 Hom.: 13541 Cov.: 20

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.432 AC: 61925 AN: 143432 Hom.: 13568 Cov.: 20 AF XY: 0.433 AC XY: 29972 AN XY: 69146

African (AFR) AF: 0.480 AC: 18405 AN: 38304

American (AMR) AF: 0.494 AC: 6937 AN: 14032

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1049 AN: 3406

East Asian (EAS) AF: 0.315 AC: 1485 AN: 4708

South Asian (SAS) AF: 0.353 AC: 1545 AN: 4372

European-Finnish (FIN) AF: 0.472 AC: 4298 AN: 9114

Middle Eastern (MID) AF: 0.239 AC: 65 AN: 272

European-Non Finnish (NFE) AF: 0.409 AC: 27157 AN: 66370

Other (OTH) AF: 0.397 AC: 779 AN: 1962

Alfa AF: 0.431 Hom.: 1781

Bravo AF: 0.434

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.53
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs7033474; hg19: chr9-37482333;