Variant 6-30060575-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_026751.2(POLR1HASP):n.366+166C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 152,166 control chromosomes in the GnomAD database, including 1,203 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 0.096 ( 1203 hom., cov: 32)

Exomes 𝑓: 0.031 ( 0 hom. )

Consequence

POLR1HASP
NR_026751.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.300

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:13924): (POLR1H antisense, pseudogene)

POLR1HASP links:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
POLR1HASP	NR_026751.2 linkuse as main transcript	n.366+166C>T	intron_variant, non_coding_transcript_variant
POLR1H	XM_047418695.1 linkuse as main transcript	c.-11+498G>A	intron_variant	XP_047274651.1
POLR1HASP	NR_145416.1 linkuse as main transcript	n.366+166C>T	intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145418.1 linkuse as main transcript	n.111+504C>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1 linkuse as main transcript	n.284+166C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0960

AC:

14592

AN:

152016

Hom.:

1197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.00440

Gnomad AMR

AF:

0.0822

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.00811

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0346

Gnomad OTH

AF:

0.111

GnomAD4 exome

AF:

0.0313

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0357

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0961

AC:

14616

AN:

152134

Hom.:

1203

Cov.:

AF XY:

0.0944

AC XY:

7025

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.0821

Gnomad4 ASJ

AF:

0.107

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.136

Gnomad4 FIN

AF:

0.00811

Gnomad4 NFE

AF:

0.0346

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.0490

Hom.:

222

Bravo

AF:

0.109

Asia WGS

AF:

0.115

AC:

402

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.3

DANN

Benign

0.64

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over