Genetic Variant PRIM2BP:n.335A>T (chr6-60425399-A-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000812929.1(ENSG00000290597):n.218A>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.173 in 1,530,890 control chromosomes in the GnomAD database, including 24,569 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 2756 hom., cov: 31)

Exomes 𝑓: 0.17 ( 21813 hom. )

Consequence

ENSG00000290597
ENST00000812929.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.00

Publications

13 publications found

Variant links:

Genes affected

PRIM2BP (HGNC:55759): (primase 2B, pseudogene)

PRIM2BP links:

ENSG00000290597 (HGNC:):

ENSG00000290597 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000812929.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812929.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
PRIM2BP	ENST00000637553.1	TSL:6	n.335A>T	non_coding_transcript_exon	Exon 4 of 9
ENSG00000290597	ENST00000812929.1		n.218A>T	non_coding_transcript_exon	Exon 3 of 8
ENSG00000290597	ENST00000812931.1		n.177A>T	non_coding_transcript_exon	Exon 3 of 7

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28031

AN:

151868

Hom.:

2749

Cov.:

show subpopulations

Gnomad AFR

AF:

0.199

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.309

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.202

GnomAD2 exomes

AF:

0.0826

AC:

14197

AN:

171900

AF XY:

0.0825

show subpopulations

Gnomad AFR exome

AF:

0.0944

Gnomad AMR exome

AF:

0.0814

Gnomad ASJ exome

AF:

0.0649

Gnomad EAS exome

AF:

0.160

Gnomad FIN exome

AF:

0.0556

Gnomad NFE exome

AF:

0.0709

Gnomad OTH exome

AF:

0.0789

GnomAD4 exome

AF:

0.172

AC:

237407

AN:

1378904

Hom.:

21813

Cov.:

AF XY:

0.174

AC XY:

118014

AN XY:

679782

show subpopulations

African (AFR)

AF:

0.203

AC:

6272

AN:

30972

American (AMR)

AF:

0.181

AC:

6227

AN:

34326

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

3989

AN:

24720

East Asian (EAS)

AF:

0.296

AC:

10449

AN:

35278

South Asian (SAS)

AF:

0.235

AC:

17496

AN:

74452

European-Finnish (FIN)

AF:

0.123

AC:

5952

AN:

48354

Middle Eastern (MID)

AF:

0.211

AC:

1177

AN:

5568

European-Non Finnish (NFE)

AF:

0.164

AC:

175402

AN:

1068168

Other (OTH)

AF:

0.183

AC:

10443

AN:

57066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

7900

15799

23699

31598

39498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6554

13108

19662

26216

32770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.185

AC:

28069

AN:

151986

Hom.:

2756

Cov.:

AF XY:

0.188

AC XY:

13967

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.199

AC:

8246

AN:

41462

American (AMR)

AF:

0.212

AC:

3235

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.175

AC:

608

AN:

3470

East Asian (EAS)

AF:

0.309

AC:

1597

AN:

5168

South Asian (SAS)

AF:

0.251

AC:

1201

AN:

4782

European-Finnish (FIN)

AF:

0.132

AC:

1392

AN:

10564

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.163

AC:

11106

AN:

67964

Other (OTH)

AF:

0.206

AC:

432

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1136

2272

3409

4545

5681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.157

Hom.:

234

Bravo

AF:

0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

-0.030

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

5.0

Varity_R

0.26

Mutation Taster

=46/54

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over