Variant rs13207351 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001318876.2(POLR1C):c.945+240786A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 291,570 control chromosomes in the GnomAD database, including 46,593 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.58 ( 26554 hom., cov: 32)

Exomes 𝑓: 0.53 ( 20039 hom. )

Consequence

POLR1C
NM_001318876.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.171

Variant links:

Genes affected

POLR1C (HGNC:):

POLR1C links:

Genome browser will be placed here

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 6-43770057-A-G is Benign according to our data. Variant chr6-43770057-A-G is described in ClinVar as [Benign]. Clinvar id is 1245515.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1C	NM_001318876.2 linkuse as main transcript	c.945+240786A>G		intron_variant			NP_001305805.1

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.583

AC:

88483

AN:

151758

Hom.:

26525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.735

Gnomad AMI

AF:

0.278

Gnomad AMR

AF:

0.607

Gnomad ASJ

AF:

0.548

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.548

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.613

GnomAD4 exome

AF:

0.528

AC:

73753

AN:

139700

Hom.:

20039

AF XY:

0.525

AC XY:

36048

AN XY:

68666

show subpopulations

Gnomad4 AFR exome

AF:

0.726

Gnomad4 AMR exome

AF:

0.588

Gnomad4 ASJ exome

AF:

0.540

Gnomad4 EAS exome

AF:

0.692

Gnomad4 SAS exome

AF:

0.537

Gnomad4 FIN exome

AF:

0.424

Gnomad4 NFE exome

AF:

0.490

Gnomad4 OTH exome

AF:

0.541

GnomAD4 genome

AF:

0.583

AC:

88568

AN:

151870

Hom.:

26554

Cov.:

AF XY:

0.582

AC XY:

43187

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.735

Gnomad4 AMR

AF:

0.607

Gnomad4 ASJ

AF:

0.548

Gnomad4 EAS

AF:

0.725

Gnomad4 SAS

AF:

0.551

Gnomad4 FIN

AF:

0.448

Gnomad4 NFE

AF:

0.502

Gnomad4 OTH

AF:

0.613

Alfa

AF:

0.358

Hom.:

831

Bravo

AF:

0.605

Asia WGS

AF:

0.606

AC:

2099

AN:

3466

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.0

DANN

Benign

0.47

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over