6-30062912-C-A

Position:

• chr6-30062912-C-A

Variant summary

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

The NM_170783.4(POLR1H):​c.356+579C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0839 in 149,490 control chromosomes in the GnomAD database, including 592 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 0.084 (592 hom., cov: 28)
• Consequence: POLR1H NM_170783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1H	NM_170783.4	c.356+579C>A		intron_variant		ENST00000332435.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR1H	ENST00000332435.10	c.356+579C>A		intron_variant		1	NM_170783.4	P1

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12528 AN: 149400 Hom.: 592 Cov.: 28

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.0442

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0392

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.0894

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0839 AC: 12542 AN: 149490 Hom.: 592 Cov.: 28 AF XY: 0.0838 AC XY: 6113 AN XY: 72964

Gnomad4 AFR AF: 0.0624

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.0391

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.0886

Alfa AF: 0.0765 Hom.: 302

Bravo AF: 0.0905

Asia WGS AF: 0.0700 AC: 244 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.62

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: rs1150740; hg19: chr6-30030689;