rs9261271

chr6-30062412-T-Achr6-30062412-T-Cchr6-30062412-T-G

Variant summary

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

The NM_170783.4(POLR1H):c.356+79T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0504 in 973,520 control chromosomes in the GnomAD database, including 1,612 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 0.052 (255 hom., cov: 32)
  • Exomes 𝑓: 0.050 (1357 hom.)
• Consequence: POLR1H NM_170783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1H	NM_170783.4	c.356+79T>A		intron_variant		ENST00000332435.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR1H	ENST00000332435.10	c.356+79T>A		intron_variant		1	NM_170783.4	P1

Frequencies

GnomAD3 genomes AF: 0.0519 AC: 7902 AN: 152166 Hom.: 254 Cov.: 32

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0598

GnomAD4 exome AF: 0.0501 AC: 41140 AN: 821236 Hom.: 1357 AF XY: 0.0497 AC XY: 21147 AN XY: 425664

Gnomad4 AFR exome AF: 0.0451

Gnomad4 AMR exome AF: 0.0496

Gnomad4 ASJ exome AF: 0.160

Gnomad4 EAS exome AF: 0.0799

Gnomad4 SAS exome AF: 0.0240

Gnomad4 FIN exome AF: 0.0242

Gnomad4 NFE exome AF: 0.0493

Gnomad4 OTH exome AF: 0.0565

GnomAD4 genome AF: 0.0520 AC: 7916 AN: 152284 Hom.: 255 Cov.: 32 AF XY: 0.0518 AC XY: 3854 AN XY: 74468

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0364

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.0236

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0570 Hom.: 37

Bravo AF: 0.0545

Asia WGS AF: 0.0360 AC: 126 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	3.5
Dann	Benign	0.66

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: rs9261271; hg19: chr6-30030189;