rs1570360

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001318876(POLR1C):c.945+240822A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 151704 control chromosomes in the gnomAD Genomes database, including 44151 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.76 ( 44151 hom., cov: 32)

Consequence

POLR1C
NM_001318876 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.275

Links

POLR1C (HGNC:):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 6:43770093-A>G is Benign according to our data. Variant chr6-43770093-A-G is described in ClinVar as [Benign]. Clinvar id is 1226235. Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1C	NM_001318876.2 linkuse as main transcript	c.945+240822A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.756

AC:

114652

AN:

151704

Hom.:

44151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.920

Gnomad AMI

AF:

0.500

Gnomad AMR

AF:

0.782

Gnomad ASJ

AF:

0.702

Gnomad EAS

AF:

0.821

Gnomad SAS

AF:

0.707

Gnomad FIN

AF:

0.635

Gnomad MID

AF:

0.688

Gnomad NFE

AF:

0.674

Gnomad OTH

AF:

0.757

GnomAD4 exome

AF:

0.706

AC:

98753

AN:

139804

Hom.:

35290

AF XY:

0.703

AC XY:

48389

AN XY:

68808

show subpopulations

Gnomad4 AFR exome

AF:

0.920

Gnomad4 AMR exome

AF:

0.754

Gnomad4 ASJ exome

AF:

0.706

Gnomad4 EAS exome

AF:

0.854

Gnomad4 SAS exome

AF:

0.696

Gnomad4 FIN exome

AF:

0.634

Gnomad4 NFE exome

AF:

0.669

Gnomad4 OTH exome

AF:

0.717

Alfa

AF:

0.693

Hom.:

29333

Bravo

AF:

0.774

Asia WGS

AF:

0.789

AC:

2734

AN:

3468

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

This variant is associated with the following publications: (PMID: 24902660, 23962084, 12067976, 23007030, 11752046, 23404364, 10626738, 21831507) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

Cadd

Benign

9.6

Dann

Benign

0.61

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over