dbSNP rs9260378: POLR1HASP:n.589-3409A>G (chr6-29950325-T-C) – 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.589-3409A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 143,758 control chromosomes in the GnomAD database, including 500 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 0.082 ( 500 hom., cov: 32)

Consequence

POLR1HASP
ENST00000849678.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89

Publications

2 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 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.589-3409A>G	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1 link	n.66-21779A>G	intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849682.1 link	n.751-21779A>G	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0820

AC:

11775

AN:

143652

Hom.:

494

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.0967

Gnomad AMR

AF:

0.0884

Gnomad ASJ

AF:

0.0813

Gnomad EAS

AF:

0.0156

Gnomad SAS

AF:

0.0486

Gnomad FIN

AF:

0.0481

Gnomad MID

AF:

0.0777

Gnomad NFE

AF:

0.0746

Gnomad OTH

AF:

0.0953

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

GnomAD4 genome

AF:

0.0821

AC:

11802

AN:

143758

Hom.:

500

Cov.:

AF XY:

0.0807

AC XY:

5688

AN XY:

70454

show subpopulations

African (AFR)

AF:

0.114

AC:

4275

AN:

37552

American (AMR)

AF:

0.0883

AC:

1258

AN:

14246

Ashkenazi Jewish (ASJ)

AF:

0.0813

AC:

265

AN:

3258

East Asian (EAS)

AF:

0.0157

AC:

AN:

4792

South Asian (SAS)

AF:

0.0487

AC:

220

AN:

4522

European-Finnish (FIN)

AF:

0.0481

AC:

504

AN:

10468

Middle Eastern (MID)

AF:

0.0797

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.0746

AC:

4908

AN:

65766

Other (OTH)

AF:

0.0950

AC:

187

AN:

1968

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

569

1139

1708

2278

2847

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

130

260

390

520

650

<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:

0.0225

Hom.:

Bravo

AF:

0.0834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.8

(source)

DANN

Benign

0.17

PhyloP100

-1.9

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