Variant rs12746 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019013.3(PIMREG):c.*664G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,194 control chromosomes in the GnomAD database, including 33,934 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 0.67 ( 33920 hom., cov: 34)

Exomes 𝑓: 0.64 ( 14 hom. )

Consequence

PIMREG
NM_019013.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0880

Variant links:

Genes affected

PIMREG (HGNC:25483): (PICALM interacting mitotic regulator) Predicted to be involved in cell division. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

PIMREG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIMREG	NM_019013.3 linkuse as main transcript	c.*664G>A		3_prime_UTR_variant	6/6	ENST00000572447.6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIMREG	ENST00000572447.6 linkuse as main transcript	c.*664G>A	3_prime_UTR_variant	6/6	1	NM_019013.3	P2	Q9BSJ6-2
PIMREG	ENST00000250056.12 linkuse as main transcript	c.*589G>A	3_prime_UTR_variant	5/5	1		A2	Q9BSJ6-1
PIMREG	ENST00000572595.6 linkuse as main transcript	c.*589G>A	3_prime_UTR_variant	6/6	3

Frequencies

GnomAD3 genomes

AF:

0.668

AC:

101529

AN:

152012

Hom.:

33885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.678

Gnomad AMI

AF:

0.606

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.720

Gnomad SAS

AF:

0.705

Gnomad FIN

AF:

0.676

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.662

Gnomad OTH

AF:

0.632

GnomAD4 exome

AF:

0.641

AC:

AN:

Hom.:

Cov.:

AF XY:

0.567

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.667

Gnomad4 NFE exome

AF:

0.705

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.668

AC:

101618

AN:

152130

Hom.:

33920

Cov.:

AF XY:

0.671

AC XY:

49905

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.679

Gnomad4 AMR

AF:

0.656

Gnomad4 ASJ

AF:

0.602

Gnomad4 EAS

AF:

0.720

Gnomad4 SAS

AF:

0.704

Gnomad4 FIN

AF:

0.676

Gnomad4 NFE

AF:

0.662

Gnomad4 OTH

AF:

0.635

Alfa

AF:

0.652

Hom.:

31297

Bravo

AF:

0.662

Asia WGS

AF:

0.697

AC:

2421

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

9.0

DANN

Benign

0.87

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over