Genetic Variant PRIM2BP:n.335A>G (chr6-60425399-A-G) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000637553.1(PRIM2BP):n.335A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.000000723 in 1,383,014 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

PRIM2BP
ENST00000637553.1 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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRIM2BP		n.60425399A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PRIM2BP	ENST00000637553.1 link	n.335A>G	non_coding_transcript_exon_variant	Exon 4 of 9	6
ENSG00000290597	ENST00000812929.1 link	n.218A>G	non_coding_transcript_exon_variant	Exon 3 of 8
ENSG00000290597	ENST00000812931.1 link	n.177A>G	non_coding_transcript_exon_variant	Exon 3 of 7

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

171900

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

7.23e-7

AC:

AN:

1383014

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

681902

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

31100

American (AMR)

AF:

0.0000290

AC:

AN:

34542

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24792

East Asian (EAS)

AF:

0.00

AC:

AN:

35388

South Asian (SAS)

AF:

0.00

AC:

AN:

74804

European-Finnish (FIN)

AF:

0.00

AC:

AN:

48442

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5588

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1071098

Other (OTH)

AF:

0.00

AC:

AN:

57260

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

0.030

CADD

Benign

(source)

DANN

Benign

0.90

PhyloP100

5.0

Varity_R

0.24

Mutation Taster

=67/33

polymorphism

(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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over