rs3132130

chr6-30059675-C-Gchr6-30059675-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000471008.5(POLR1H):n.777C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,296 control chromosomes in the GnomAD database, including 61,603 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 0.90 (61603 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: POLR1H ENST00000471008.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

Genes affected

POLR1H (HGNC:13182): (RNA polymerase I subunit H) This gene encodes a DNA-directed RNA polymerase I subunit. The encoded protein contains two potential zinc-binding motifs and may play a role in regulation of cell proliferation. The encoded protein may be involved in cancer and human immunodeficiency virus progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1HASP	NR_026751.2	n.366+1066G>C		intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145416.1	n.366+1066G>C		intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145418.1	n.111+1404G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.284+1066G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136727 AN: 152178 Hom.: 61540 Cov.: 33

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.894

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.899 AC: 136849 AN: 152296 Hom.: 61603 Cov.: 33 AF XY: 0.900 AC XY: 66991 AN XY: 74470

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.895

Alfa AF: 0.876 Hom.: 6812

Bravo AF: 0.903

Asia WGS AF: 0.961 AC: 3341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.1
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132130; hg19: chr6-30027452;