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rs1570360

Variant summary

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

The NM_001318876.2(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 0.732 in 291,618 control chromosomes in the GnomAD database, including 79,500 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.76 ( 44210 hom., cov: 32)
Exomes 𝑓: 0.71 ( 35290 hom. )

Consequence

POLR1C
NM_001318876.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.275
Variant links:
Genes affected

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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
GnomAd4 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
POLR1CNM_001318876.2 linkuse as main transcriptc.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.:
32
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
GnomAD4 genome
AF:
0.756
AC:
114765
AN:
151814
Hom.:
44210
Cov.:
32
AF XY:
0.755
AC XY:
56029
AN XY:
74190
show subpopulations
Gnomad4 AFR
AF:
0.920
Gnomad4 AMR
AF:
0.782
Gnomad4 ASJ
AF:
0.702
Gnomad4 EAS
AF:
0.821
Gnomad4 SAS
AF:
0.705
Gnomad4 FIN
AF:
0.635
Gnomad4 NFE
AF:
0.674
Gnomad4 OTH
AF:
0.758
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 submitterclinical testingGeneDxJun 19, 2021This 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
9.3
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.

Other links and lift over

dbSNP: rs1570360; hg19: chr6-43737830; API