chr6-30064718-A-G

Position:

• chr6-30064718-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_170783.4(POLR1H):​c.*21A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,605,336 control chromosomes in the GnomAD database, including 15,601 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 0.17 (2725 hom., cov: 32)
  • Exomes 𝑓: 0.12 (12876 hom.)
• Consequence: POLR1H NM_170783.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

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]

PPP1R11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1H	NM_170783.4	c.*21A>G		3_prime_UTR_variant	4/4	ENST00000332435.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR1H	ENST00000332435.10	c.*21A>G		3_prime_UTR_variant	4/4	1	NM_170783.4	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25851 AN: 151996 Hom.: 2710 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.192

GnomAD3 exomes AF: 0.149 AC: 35981 AN: 241038 Hom.: 3360 AF XY: 0.146 AC XY: 19207 AN XY: 131722

Gnomad AFR exome AF: 0.266

Gnomad AMR exome AF: 0.219

Gnomad ASJ exome AF: 0.295

Gnomad EAS exome AF: 0.201

Gnomad SAS exome AF: 0.154

Gnomad FIN exome AF: 0.0478

Gnomad NFE exome AF: 0.110

Gnomad OTH exome AF: 0.146

GnomAD4 exome AF: 0.120 AC: 174036 AN: 1453224 Hom.: 12876 Cov.: 29 AF XY: 0.121 AC XY: 87633 AN XY: 723144

Gnomad4 AFR exome AF: 0.273

Gnomad4 AMR exome AF: 0.220

Gnomad4 ASJ exome AF: 0.293

Gnomad4 EAS exome AF: 0.248

Gnomad4 SAS exome AF: 0.165

Gnomad4 FIN exome AF: 0.0499

Gnomad4 NFE exome AF: 0.101

Gnomad4 OTH exome AF: 0.144

GnomAD4 genome AF: 0.170 AC: 25895 AN: 152112 Hom.: 2725 Cov.: 32 AF XY: 0.168 AC XY: 12514 AN XY: 74356

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0479

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.189

Alfa AF: 0.154 Hom.: 870

Bravo AF: 0.190

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.93
DANN	Benign	0.76
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1048412; hg19: chr6-30032495; COSMIC: COSV60138184; COSMIC: COSV60138184;