rs3132130

Variant names:

• chr6-30059675-C-G
• rs3132130
• ENST00000471008.5:n.777C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-30059675-C-G
• chr6-30059675-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.366+1066G>C		intron_variant	Intron 2 of 5
POLR1HASP	NR_145416.1	n.366+1066G>C		intron_variant	Intron 2 of 6
POLR1HASP	NR_145418.1	n.111+1404G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1H	ENST00000471008.5	n.777C>G		non_coding_transcript_exon_variant	Exon 1 of 2	1
POLR1HASP	ENST00000420251.5	n.361+1066G>C		intron_variant	Intron 2 of 5	1
POLR1HASP	ENST00000431012.5	n.101+1404G>C		intron_variant	Intron 1 of 2	1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.919 AC: 38202 AN: 41554

American (AMR) AF: 0.917 AC: 14032 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3149 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5124 AN: 5192

South Asian (SAS) AF: 0.945 AC: 4565 AN: 4830

European-Finnish (FIN) AF: 0.890 AC: 9424 AN: 10592

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59332 AN: 68026

Other (OTH) AF: 0.895 AC: 1893 AN: 2116

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
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs3132130; hg19: chr6-30027452;