6-43751654-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001318876.2(POLR1C):​c.945+222383G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,092 control chromosomes in the GnomAD database, including 8,386 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 0.33 ( 8386 hom., cov: 33)

Consequence

POLR1C
NM_001318876.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0770
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
POLR1CNM_001318876.2 linkuse as main transcriptc.945+222383G>T intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.329
AC:
49938
AN:
151974
Hom.:
8373
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.292
Gnomad AMI
AF:
0.384
Gnomad AMR
AF:
0.252
Gnomad ASJ
AF:
0.418
Gnomad EAS
AF:
0.237
Gnomad SAS
AF:
0.367
Gnomad FIN
AF:
0.379
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.359
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.329
AC:
49996
AN:
152092
Hom.:
8386
Cov.:
33
AF XY:
0.326
AC XY:
24260
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.292
Gnomad4 AMR
AF:
0.253
Gnomad4 ASJ
AF:
0.418
Gnomad4 EAS
AF:
0.237
Gnomad4 SAS
AF:
0.368
Gnomad4 FIN
AF:
0.379
Gnomad4 NFE
AF:
0.359
Gnomad4 OTH
AF:
0.317
Alfa
AF:
0.349
Hom.:
12459
Bravo
AF:
0.316
Asia WGS
AF:
0.291
AC:
1013
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
7.2
DANN
Benign
0.70

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: rs9394963; hg19: chr6-43719391; API