dbSNP rs6457116: POLR1HASP:n.589-23332C>T (chr6-29970248-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000849678.1(POLR1HASP):n.589-23332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 152,222 control chromosomes in the GnomAD database, including 277 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 0.051 ( 277 hom., cov: 32)

Consequence

POLR1HASP
ENST00000849678.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.792

Publications

8 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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0822 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	ENST00000849678.1 link	n.589-23332C>T	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1 link	n.65+6355C>T	intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1 link	n.506-13498C>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0515

AC:

7827

AN:

152104

Hom.:

278

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0846

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0860

Gnomad ASJ

AF:

0.0337

Gnomad EAS

AF:

0.00424

Gnomad SAS

AF:

0.0456

Gnomad FIN

AF:

0.0444

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0303

Gnomad OTH

AF:

0.0498

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0515

AC:

7838

AN:

152222

Hom.:

277

Cov.:

AF XY:

0.0514

AC XY:

3826

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0845

AC:

3511

AN:

41530

American (AMR)

AF:

0.0860

AC:

1315

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0337

AC:

117

AN:

3472

East Asian (EAS)

AF:

0.00425

AC:

AN:

5182

South Asian (SAS)

AF:

0.0461

AC:

222

AN:

4816

European-Finnish (FIN)

AF:

0.0444

AC:

471

AN:

10608

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0303

AC:

2063

AN:

68002

Other (OTH)

AF:

0.0488

AC:

103

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

373

747

1120

1494

1867

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0375

Hom.:

115

Bravo

AF:

0.0563

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.90

(source)

DANN

Benign

0.17

PhyloP100

-0.79

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