Variant rs714549 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_006204.4(PDE6C):c.1119+21A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,561,552 control chromosomes in the GnomAD database, including 90,574 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 10582 hom., cov: 32)

Exomes 𝑓: 0.33 ( 79992 hom. )

Consequence

PDE6C
NM_006204.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.251

Variant links:

Genes affected

PDE6C (HGNC:8787): (phosphodiesterase 6C) This gene encodes the alpha-prime subunit of cone phosphodiesterase, which is composed of a homodimer of two alpha-prime subunits and 3 smaller proteins of 11, 13, and 15 kDa. Mutations in this gene are associated with cone dystrophy type 4 (COD4). [provided by RefSeq, Mar 2010]

PDE6C 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=-0.89).

BP6

Variant 10-93629326-A-G is Benign according to our data. Variant chr10-93629326-A-G is described in ClinVar as [Benign]. Clinvar id is 259939.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE6C	NM_006204.4 linkuse as main transcript	c.1119+21A>G		intron_variant		ENST00000371447.4	NP_006195.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE6C	ENST00000371447.4 linkuse as main transcript	c.1119+21A>G		intron_variant		1	NM_006204.4	ENSP00000360502	P1

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

56080

AN:

151858

Hom.:

10560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.429

Gnomad AMI

AF:

0.428

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.466

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.326

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.335

Gnomad OTH

AF:

0.350

GnomAD3 exomes

AF:

0.355

AC:

89142

AN:

251204

Hom.:

16352

AF XY:

0.349

AC XY:

47347

AN XY:

135774

show subpopulations

Gnomad AFR exome

AF:

0.435

Gnomad AMR exome

AF:

0.399

Gnomad ASJ exome

AF:

0.329

Gnomad EAS exome

AF:

0.459

Gnomad SAS exome

AF:

0.308

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.334

Gnomad OTH exome

AF:

0.330

GnomAD4 exome

AF:

0.333

AC:

469567

AN:

1409576

Hom.:

79992

Cov.:

AF XY:

0.333

AC XY:

234598

AN XY:

704372

show subpopulations

Gnomad4 AFR exome

AF:

0.422

Gnomad4 AMR exome

AF:

0.398

Gnomad4 ASJ exome

AF:

0.324

Gnomad4 EAS exome

AF:

0.465

Gnomad4 SAS exome

AF:

0.308

Gnomad4 FIN exome

AF:

0.330

Gnomad4 NFE exome

AF:

0.324

Gnomad4 OTH exome

AF:

0.348

GnomAD4 genome

AF:

0.369

AC:

56152

AN:

151976

Hom.:

10582

Cov.:

AF XY:

0.368

AC XY:

27360

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.429

Gnomad4 AMR

AF:

0.388

Gnomad4 ASJ

AF:

0.316

Gnomad4 EAS

AF:

0.466

Gnomad4 SAS

AF:

0.306

Gnomad4 FIN

AF:

0.326

Gnomad4 NFE

AF:

0.335

Gnomad4 OTH

AF:

0.352

Alfa

AF:

0.346

Hom.:

2043

Bravo

AF:

0.379

Asia WGS

AF:

0.409

AC:

1422

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.0

DANN

Benign

0.66

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