rs833052

chr6-43755598-A-Cchr6-43755598-A-Gchr6-43755598-A-T

Variant summary

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

The NM_001318876.2(POLR1C):c.945+226327A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,228 control chromosomes in the GnomAD database, including 59,177 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 0.88 (59177 hom., cov: 31)
• Consequence: POLR1C NM_001318876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.945+226327A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133808 AN: 152110 Hom.: 59113 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.880 AC: 133925 AN: 152228 Hom.: 59177 Cov.: 31 AF XY: 0.877 AC XY: 65268 AN XY: 74422

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.877

Alfa AF: 0.871 Hom.: 54021

Bravo AF: 0.884

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.51
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs833052; hg19: chr6-43723335;