6-29982433-A-G

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-5038T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,518 control chromosomes in the GnomAD database, including 4,554 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 0.23 ( 4554 hom., cov: 32)

Consequence

POLR1HASP
ENST00000688495.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700
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=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
POLR1HASPENST00000688495.1 linkn.361-5038T>C intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.234
AC:
35370
AN:
151408
Hom.:
4544
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.118
Gnomad AMI
AF:
0.426
Gnomad AMR
AF:
0.229
Gnomad ASJ
AF:
0.231
Gnomad EAS
AF:
0.292
Gnomad SAS
AF:
0.296
Gnomad FIN
AF:
0.328
Gnomad MID
AF:
0.264
Gnomad NFE
AF:
0.279
Gnomad OTH
AF:
0.217
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.234
AC:
35389
AN:
151518
Hom.:
4554
Cov.:
32
AF XY:
0.237
AC XY:
17546
AN XY:
74000
show subpopulations
Gnomad4 AFR
AF:
0.118
Gnomad4 AMR
AF:
0.229
Gnomad4 ASJ
AF:
0.231
Gnomad4 EAS
AF:
0.291
Gnomad4 SAS
AF:
0.295
Gnomad4 FIN
AF:
0.328
Gnomad4 NFE
AF:
0.279
Gnomad4 OTH
AF:
0.223
Alfa
AF:
0.264
Hom.:
3629
Bravo
AF:
0.219
Asia WGS
AF:
0.313
AC:
1089
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.0
DANN
Benign
0.48

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: rs401618; hg19: chr6-29950210; API