rs9369421

chr6-43794385-T-C

Variant summary

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

The NM_001318876.2(POLR1C):c.945+265114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,220 control chromosomes in the GnomAD database, including 1,809 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 0.13 (1809 hom., cov: 33)
• Consequence: POLR1C NM_001318876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

Genes affected

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.945+265114T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20523 AN: 152102 Hom.: 1805 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0882

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0822

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.135 AC: 20541 AN: 152220 Hom.: 1809 Cov.: 33 AF XY: 0.135 AC XY: 10044 AN XY: 74440

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.0881

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.0822

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0831 Hom.: 417

Bravo AF: 0.140

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.95
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9369421; hg19: chr6-43762122;