Variant chr16-29819546-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024516.4(PAGR1):c.566-9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00403 in 1,613,926 control chromosomes in the GnomAD database, including 175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0056 ( 19 hom., cov: 32)

Exomes 𝑓: 0.0039 ( 156 hom. )

Consequence

PAGR1
NM_024516.4 intron

Scores

Splicing: ADA: 0.0002277

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.679

Variant links:

Genes affected

PAGR1 (HGNC:28707): (PAXIP1 associated glutamate rich protein 1) Enables estrogen receptor binding activity. Involved in positive regulation of cell cycle G1/S phase transition; positive regulation of intracellular estrogen receptor signaling pathway; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Part of MLL3/4 complex. [provided by Alliance of Genome Resources, Apr 2022]

PAGR1 links:

MVP-DT (HGNC:):

MVP-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 16-29819546-C-T is Benign according to our data. Variant chr16-29819546-C-T is described in ClinVar as [Benign]. Clinvar id is 716597.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAGR1	NM_024516.4 linkuse as main transcript	c.566-9C>T		intron_variant		ENST00000320330.8	NP_078792.1	Q9BTK6
MVP-DT	NR_186424.1 linkuse as main transcript	n.240G>A		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
PAGR1	ENST00000320330.8 linkuse as main transcript	c.566-9C>T	intron_variant	1	NM_024516.4	ENSP00000326519.6	Q9BTK6
ENSG00000281348	ENST00000562285.1 linkuse as main transcript	n.53-9C>T	intron_variant	2		ENSP00000457363.1	H3BTX0
ENSG00000280893	ENST00000609618.2 linkuse as main transcript	n.*507-9C>T	intron_variant	5		ENSP00000476774.2	A0A0G2JLL6

Frequencies

GnomAD3 genomes

AF:

0.00567

AC:

863

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000917

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0767

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.0303

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000838

Gnomad OTH

AF:

0.00717

GnomAD3 exomes

AF:

0.00950

AC:

2384

AN:

251070

Hom.:

AF XY:

0.00869

AC XY:

1180

AN XY:

135746

show subpopulations

Gnomad AFR exome

AF:

0.000923

Gnomad AMR exome

AF:

0.00133

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0801

Gnomad SAS exome

AF:

0.00118

Gnomad FIN exome

AF:

0.0294

Gnomad NFE exome

AF:

0.00114

Gnomad OTH exome

AF:

0.00816

GnomAD4 exome

AF:

0.00386

AC:

5644

AN:

1461648

Hom.:

156

Cov.:

AF XY:

0.00380

AC XY:

2763

AN XY:

727096

show subpopulations

Gnomad4 AFR exome

AF:

0.000478

Gnomad4 AMR exome

AF:

0.00125

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0776

Gnomad4 SAS exome

AF:

0.00112

Gnomad4 FIN exome

AF:

0.0298

Gnomad4 NFE exome

AF:

0.000371

Gnomad4 OTH exome

AF:

0.00646

GnomAD4 genome

AF:

0.00565

AC:

860

AN:

152278

Hom.:

Cov.:

AF XY:

0.00721

AC XY:

537

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.000914

Gnomad4 AMR

AF:

0.00164

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0765

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0303

Gnomad4 NFE

AF:

0.000838

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00109

Hom.:

Bravo

AF:

0.00417

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.000327

EpiControl

AF:

0.000415

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00023

dbscSNV1_RF

Benign

0.010

SpliceAI score (max)

0.11

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over