Variant 5-123090166-A-AGCCGCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2

The NM_001136239.4(PRDM6):c.162_167dupGCCGCC(p.Pro55_Pro56dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00815 in 1,488,890 control chromosomes in the GnomAD database, including 67 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0070 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0083 ( 62 hom. )

Consequence

PRDM6
NM_001136239.4 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.42

Variant links:

Genes affected

PRDM6 (HGNC:9350): (PR/SET domain 6) The protein encoded by this gene is a transcriptional repressor and a member of the PRDM family. Family members contain a PR domain and multiple zinc-finger domains. The encoded protein is involved in regulation of vascular smooth muscle cells (VSMC) contractile proteins. Mutations in this gene result in patent ductus arteriosus 3 (PDA3). [provided by RefSeq, Apr 2017]

PRDM6 links:

PRDM6-AS1 (HGNC:55869): (PRDM6 antisense RNA 1)

PRDM6-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001136239.4.

BP6

Variant 5-123090166-A-AGCCGCC is Benign according to our data. Variant chr5-123090166-A-AGCCGCC is described in ClinVar as [Likely_benign]. Clinvar id is 2655659.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 1043 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRDM6	NM_001136239.4 link	c.162_167dupGCCGCC	p.Pro55_Pro56dup	disruptive_inframe_insertion	2/8	ENST00000407847.5	NP_001129711.1	Q9NQX0-3
PRDM6	XM_047417878.1 link	c.162_167dupGCCGCC	p.Pro55_Pro56dup	disruptive_inframe_insertion	2/4		XP_047273834.1
PRDM6-AS1	NR_146771.1 link	n.145_150dupGGCGGC		non_coding_transcript_exon_variant	1/2
PRDM6	XR_001742346.2 link	n.456_461dupGCCGCC		non_coding_transcript_exon_variant	2/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDM6	ENST00000407847.5 link	c.162_167dupGCCGCC	p.Pro55_Pro56dup	disruptive_inframe_insertion	2/8	5	NM_001136239.4	ENSP00000384725.3		Q9NQX0-3
PRDM6-AS1	ENST00000458103.2 link	n.128_133dupGGCGGC		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.00703

AC:

1044

AN:

148450

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00186

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0108

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.000778

Gnomad SAS

AF:

0.00187

Gnomad FIN

AF:

0.00398

Gnomad MID

AF:

0.0255

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.00880

GnomAD3 exomes

AF:

0.00275

AC:

240

AN:

87172

Hom.:

AF XY:

0.00293

AC XY:

145

AN XY:

49466

show subpopulations

Gnomad AFR exome

AF:

0.00104

Gnomad AMR exome

AF:

0.00137

Gnomad ASJ exome

AF:

0.00323

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000788

Gnomad FIN exome

AF:

0.00275

Gnomad NFE exome

AF:

0.00481

Gnomad OTH exome

AF:

0.00251

GnomAD4 exome

AF:

0.00828

AC:

11093

AN:

1340326

Hom.:

Cov.:

AF XY:

0.00806

AC XY:

5322

AN XY:

660634

show subpopulations

Gnomad4 AFR exome

AF:

0.00159

Gnomad4 AMR exome

AF:

0.00427

Gnomad4 ASJ exome

AF:

0.00850

Gnomad4 EAS exome

AF:

0.000579

Gnomad4 SAS exome

AF:

0.00173

Gnomad4 FIN exome

AF:

0.00534

Gnomad4 NFE exome

AF:

0.00931

Gnomad4 OTH exome

AF:

0.00827

GnomAD4 genome

AF:

0.00702

AC:

1043

AN:

148564

Hom.:

Cov.:

AF XY:

0.00664

AC XY:

483

AN XY:

72736

show subpopulations

Gnomad4 AFR

AF:

0.00185

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.000780

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00398

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.00870

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2023

PRDM6: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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