dbSNP rs7769930: POLR1HASP:n.611T>G (chr6-30061030-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000437417.5(POLR1HASP):n.611T>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 0.147 in 153,862 control chromosomes in the GnomAD database, including 2,242 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 0.15 ( 2235 hom., cov: 33)

Exomes 𝑓: 0.074 ( 7 hom. )

Consequence

POLR1HASP
ENST00000437417.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.352

Publications

14 publications found

Variant links:

Genes affected

POLR1HASP (HGNC:):

POLR1HASP links:

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:13924): (POLR1H antisense, pseudogene)

POLR1HASP links:

PPP1R11 (HGNC:9285): (protein phosphatase 1 regulatory inhibitor subunit 11) This gene encodes a specific inhibitor of protein phosphatase-1 (PP1) with a differential sensitivity toward the metal-independent and metal-dependent forms of PP1. The gene is located within the major histocompatibility complex class I region on chromosome 6. [provided by RefSeq, Jul 2008]

PPP1R11 links:

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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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437417.5. 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.112-35T>G	intron	N/A
POLR1HASP	NR_145416.1	n.112-35T>G	intron	N/A
POLR1HASP	NR_145418.1	n.111+49T>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
POLR1HASP	ENST00000437417.5	TSL:1	n.611T>G	non_coding_transcript_exon	Exon 1 of 6
POLR1H	ENST00000471008.5	TSL:1	n.2132A>C	non_coding_transcript_exon	Exon 1 of 2
POLR1HASP	ENST00000420251.5	TSL:1	n.107-35T>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22505

AN:

152114

Hom.:

2225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.150

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.0318

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.0861

Gnomad OTH

AF:

0.172

GnomAD4 exome

AF:

0.0742

AC:

121

AN:

1630

Hom.:

Cov.:

AF XY:

0.0831

AC XY:

AN XY:

866

show subpopulations

African (AFR)

AF:

0.241

AC:

AN:

American (AMR)

AF:

0.111

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.118

AC:

AN:

South Asian (SAS)

AF:

0.0924

AC:

AN:

238

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0540

AC:

AN:

1092

Other (OTH)

AF:

0.0333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.536

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.148

AC:

22543

AN:

152232

Hom.:

2235

Cov.:

AF XY:

0.146

AC XY:

10883

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.267

AC:

11078

AN:

41490

American (AMR)

AF:

0.150

AC:

2295

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.281

AC:

974

AN:

3468

East Asian (EAS)

AF:

0.154

AC:

798

AN:

5186

South Asian (SAS)

AF:

0.160

AC:

773

AN:

4830

European-Finnish (FIN)

AF:

0.0318

AC:

338

AN:

10624

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0861

AC:

5857

AN:

68016

Other (OTH)

AF:

0.168

AC:

356

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

945

1889

2834

3778

4723

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.116

Hom.:

2533

Bravo

AF:

0.164

Asia WGS

AF:

0.152

AC:

528

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.7

(source)

DANN

Benign

0.46

PhyloP100

0.35

PromoterAI

-0.034

Neutral

(source)

Splicing

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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over