Genetic Variant POLR1HASP:n.361-5038T>C (chr6-29982433-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

24 publications found

Variant links:

Genes affected

POLR1HASP (HGNC:):

POLR1HASP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank
POLR1HASP	ENST00000688495.1 link	n.361-5038T>C	intron_variant	Intron 3 of 3
POLR1HASP	ENST00000849678.1 link	n.589-35517T>C	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849680.1 link	n.506-25683T>C	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35370

AN:

151408

Hom.:

4544

Cov.:

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.:

AF XY:

0.237

AC XY:

17546

AN XY:

74000

show subpopulations

African (AFR)

AF:

0.118

AC:

4879

AN:

41210

American (AMR)

AF:

0.229

AC:

3485

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

801

AN:

3468

East Asian (EAS)

AF:

0.291

AC:

1503

AN:

5160

South Asian (SAS)

AF:

0.295

AC:

1420

AN:

4814

European-Finnish (FIN)

AF:

0.328

AC:

3430

AN:

10472

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.279

AC:

18938

AN:

67872

Other (OTH)

AF:

0.223

AC:

469

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1306

2613

3919

5226

6532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.263

Hom.:

15054

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

(source)

DANN

Benign

0.48

PhyloP100

-0.0070

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over