rs6899540

Positions:

• chr6-43790587-A-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+261316A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,110 control chromosomes in the GnomAD database, including 2,094 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 0.16 (2094 hom., cov: 32)
• Consequence: POLR1C NM_001318876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.945+261316A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24232 AN: 151992 Hom.: 2084 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.160 AC: 24273 AN: 152110 Hom.: 2094 Cov.: 32 AF XY: 0.154 AC XY: 11487 AN XY: 74370

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0740

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.156

Alfa AF: 0.164 Hom.: 623

Bravo AF: 0.160

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6899540; hg19: chr6-43758324;