rs6900017

chr6-43790748-C-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+261477C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,158 control chromosomes in the GnomAD database, including 1,704 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 (1704 hom., cov: 32)
• Consequence: POLR1C NM_001318876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

Genes affected

POLR1C (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 = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.945+261477C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19848 AN: 152040 Hom.: 1701 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0689

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.131 AC: 19866 AN: 152158 Hom.: 1704 Cov.: 32 AF XY: 0.130 AC XY: 9671 AN XY: 74416

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.0875

Gnomad4 ASJ AF: 0.0911

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0689

Gnomad4 NFE AF: 0.0804

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0876 Hom.: 1312

Bravo AF: 0.136

Asia WGS AF: 0.169 AC: 589 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	3.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6900017; hg19: chr6-43758485;