rs6905288

chr6-43791136-G-Achr6-43791136-G-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+261865G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,022 control chromosomes in the GnomAD database, including 24,805 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 0.57 (24805 hom., cov: 33)
• Consequence: POLR1C NM_001318876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

Genes affected

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.945+261865G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86012 AN: 151904 Hom.: 24770 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.566 AC: 86095 AN: 152022 Hom.: 24805 Cov.: 33 AF XY: 0.575 AC XY: 42734 AN XY: 74314

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.576

Alfa AF: 0.575 Hom.: 38617

Bravo AF: 0.559

Asia WGS AF: 0.722 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.1
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6905288; hg19: chr6-43758873;