Variant chr4-761398-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_006315.7(PCGF3):c.582C>T(p.Asn194=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 1,608,522 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0045 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0030 ( 13 hom. )

Consequence

PCGF3
NM_006315.7 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.918

Variant links:

Genes affected

PCGF3 (HGNC:10066): (polycomb group ring finger 3) The protein encoded by this gene contains a C3HC4 type RING finger, which is a motif known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. [provided by RefSeq, Jul 2008]

PCGF3 links:

LOC124900163 (HGNC:):

LOC124900163 links:

PCGF3-AS1 (HGNC:56108): (PCGF3 antisense RNA 1)

PCGF3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 4-761398-C-T is Benign according to our data. Variant chr4-761398-C-T is described in ClinVar as [Benign]. Clinvar id is 769626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.918 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PCGF3	NM_006315.7 linkuse as main transcript	c.582C>T	p.Asn194=	synonymous_variant	9/11	ENST00000362003.10
LOC124900163	XM_047416474.1 linkuse as main transcript	c.-1351G>A		5_prime_UTR_variant	2/2
PCGF3-AS1	NR_171661.1 linkuse as main transcript	n.3426G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCGF3	ENST00000362003.10 linkuse as main transcript	c.582C>T	p.Asn194=	synonymous_variant	9/11	5	NM_006315.7	P1	Q3KNV8-1
PCGF3-AS1	ENST00000660016.1 linkuse as main transcript	n.1421G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes

AF:

0.00447

AC:

680

AN:

152256

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00543

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000589

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0124

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00451

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00313

AC:

766

AN:

244652

Hom.:

AF XY:

0.00304

AC XY:

404

AN XY:

132976

show subpopulations

Gnomad AFR exome

AF:

0.00673

Gnomad AMR exome

AF:

0.000635

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000571

Gnomad SAS exome

AF:

0.000609

Gnomad FIN exome

AF:

0.0111

Gnomad NFE exome

AF:

0.00335

Gnomad OTH exome

AF:

0.00153

GnomAD4 exome

AF:

0.00298

AC:

4342

AN:

1456148

Hom.:

Cov.:

AF XY:

0.00301

AC XY:

2182

AN XY:

724026

show subpopulations

Gnomad4 AFR exome

AF:

0.00628

Gnomad4 AMR exome

AF:

0.000637

Gnomad4 ASJ exome

AF:

0.000308

Gnomad4 EAS exome

AF:

0.0000510

Gnomad4 SAS exome

AF:

0.000574

Gnomad4 FIN exome

AF:

0.0109

Gnomad4 NFE exome

AF:

0.00301

Gnomad4 OTH exome

AF:

0.00218

GnomAD4 genome

AF:

0.00448

AC:

682

AN:

152374

Hom.:

Cov.:

AF XY:

0.00484

AC XY:

361

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00543

Gnomad4 AMR

AF:

0.000588

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0124

Gnomad4 NFE

AF:

0.00451

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00343

Hom.:

Bravo

AF:

0.00338

Asia WGS

AF:

0.00115

AC:

AN:

3478

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 30, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over