rs699947

chr6-43768652-A-Cchr6-43768652-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_001318876.2(POLR1C):c.945+239381A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,102 control chromosomes in the GnomAD database, including 28,280 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.60 (28280 hom., cov: 33)
• Consequence: POLR1C NM_001318876.2 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 1.03

Genes affected

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 6-43768652-A-C is Benign according to our data. Variant chr6-43768652-A-C is described in ClinVar as [Benign]. Clinvar id is 12224.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2	c.945+239381A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90793 AN: 151984 Hom.: 28251 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.597 AC: 90880 AN: 152102 Hom.: 28280 Cov.: 33 AF XY: 0.595 AC XY: 44239 AN XY: 74346

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.616

Alfa AF: 0.503 Hom.: 3587

Bravo AF: 0.623

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Atherosclerosis, susceptibility to Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Dec 01, 2009

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.1
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs699947; hg19: chr6-43736389;