dbSNP rs3132130: POLR1H:n.777C>G (chr6-30059675-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0590

Publications

10 publications found

Variant links:

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]

POLR1H links:

POLR1HASP (HGNC:):

POLR1HASP links:

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

POLR1HASP links:

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new If you want to explore the variant's impact on the transcript ENST00000471008.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000471008.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
POLR1HASP	NR_026751.2	n.366+1066G>C	intron	N/A
POLR1HASP	NR_145416.1	n.366+1066G>C	intron	N/A
POLR1HASP	NR_145418.1	n.111+1404G>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
POLR1H	ENST00000471008.5	TSL:1	n.777C>G	non_coding_transcript_exon	Exon 1 of 2
POLR1HASP	ENST00000420251.5	TSL:1	n.361+1066G>C	intron	N/A
POLR1HASP	ENST00000431012.5	TSL:1	n.101+1404G>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.898

AC:

136727

AN:

152178

Hom.:

61540

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.899

AC:

136849

AN:

152296

Hom.:

61603

Cov.:

AF XY:

0.900

AC XY:

66991

AN XY:

74470

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

721

1443

2164

2886

3607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

3.1

(source)

DANN

Benign

0.61

PhyloP100

-0.059

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over