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rs7769930

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.352
Variant links:
Genes affected
POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
POLR1HASPNR_026751.2 linkuse as main transcriptn.112-35T>G intron_variant, non_coding_transcript_variant
POLR1HXM_047418695.1 linkuse as main transcriptc.-10-485A>C intron_variant
POLR1HASPNR_145416.1 linkuse as main transcriptn.112-35T>G intron_variant, non_coding_transcript_variant
POLR1HASPNR_145418.1 linkuse as main transcriptn.111+49T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
POLR1HASPENST00000688495.1 linkuse as main transcriptn.30-35T>G intron_variant, non_coding_transcript_variant
ENST00000611686.1 linkuse as main transcript upstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.148
AC:
22505
AN:
152114
Hom.:
2225
Cov.:
33
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.:
7
Cov.:
0
AF XY:
0.0831
AC XY:
72
AN XY:
866
show subpopulations
Gnomad4 AFR exome
AF:
0.241
Gnomad4 AMR exome
AF:
0.111
Gnomad4 ASJ exome
AF:
0.250
Gnomad4 EAS exome
AF:
0.118
Gnomad4 SAS exome
AF:
0.0924
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0540
Gnomad4 OTH exome
AF:
0.0333
GnomAD4 genome
AF:
0.148
AC:
22543
AN:
152232
Hom.:
2235
Cov.:
33
AF XY:
0.146
AC XY:
10883
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.267
Gnomad4 AMR
AF:
0.150
Gnomad4 ASJ
AF:
0.281
Gnomad4 EAS
AF:
0.154
Gnomad4 SAS
AF:
0.160
Gnomad4 FIN
AF:
0.0318
Gnomad4 NFE
AF:
0.0861
Gnomad4 OTH
AF:
0.168
Alfa
AF:
0.116
Hom.:
535
Bravo
AF:
0.164
Asia WGS
AF:
0.152
AC:
528
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
8.7
Dann
Benign
0.46

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7769930; hg19: chr6-30028807; API