6-44239013-G-A

Position:

• chr6-44239013-G-A

Variant summary

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

The NM_001318876.2(POLR1C):​c.946-202877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,146 control chromosomes in the GnomAD database, including 2,315 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 0.15 (2315 hom., cov: 32)
• Consequence: POLR1C NM_001318876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.946-202877G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23234 AN: 152028 Hom.: 2315 Cov.: 32

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.153 AC: 23232 AN: 152146 Hom.: 2315 Cov.: 32 AF XY: 0.157 AC XY: 11668 AN XY: 74374

Gnomad4 AFR AF: 0.0437

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.152

Alfa AF: 0.178 Hom.: 3630

Bravo AF: 0.154

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9472236; hg19: chr6-44206750;