rs3869068

Variant summary

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

The NR_026751.2(POLR1HASP):​n.443-292G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,084 control chromosomes in the GnomAD database, including 2,739 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 0.17 ( 2739 hom., cov: 32)

Consequence

POLR1HASP
NR_026751.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.07
Variant links:
Genes affected
POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

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=-1.07).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
POLR1HASPNR_026751.2 linkuse as main transcriptn.443-292G>A intron_variant, non_coding_transcript_variant
POLR1HASPNR_145416.1 linkuse as main transcriptn.443-292G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
POLR1HASPENST00000688495.1 linkuse as main transcriptn.360+21840G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.170
AC:
25883
AN:
151966
Hom.:
2722
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.274
Gnomad AMI
AF:
0.0252
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.303
Gnomad EAS
AF:
0.189
Gnomad SAS
AF:
0.181
Gnomad FIN
AF:
0.0476
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.109
Gnomad OTH
AF:
0.194
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.171
AC:
25935
AN:
152084
Hom.:
2739
Cov.:
32
AF XY:
0.168
AC XY:
12529
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.274
Gnomad4 AMR
AF:
0.211
Gnomad4 ASJ
AF:
0.303
Gnomad4 EAS
AF:
0.190
Gnomad4 SAS
AF:
0.183
Gnomad4 FIN
AF:
0.0476
Gnomad4 NFE
AF:
0.109
Gnomad4 OTH
AF:
0.193
Alfa
AF:
0.135
Hom.:
2916
Bravo
AF:
0.191
Asia WGS
AF:
0.210
AC:
732
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.81
DANN
Benign
0.29

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: rs3869068; hg19: chr6-30004052; API