rs8069344

Variant summary

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

The NM_000180.4(GUCY2D):c.2345T>A(p.Leu782His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,613,268 control chromosomes in the GnomAD database, including 17,920 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Synonymous variant affecting the same amino acid position (i.e. L782L) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.19 ( 4051 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13869 hom. )

Consequence

GUCY2D
NM_000180.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 2.36

Variant links:

Genes affected

GUCY2D (HGNC:4689): (guanylate cyclase 2D, retinal) This gene encodes a retina-specific guanylate cyclase, which is a member of the membrane guanylyl cyclase family. Like other membrane guanylyl cyclases, this enzyme has a hydrophobic amino-terminal signal sequence followed by a large extracellular domain, a single membrane spanning domain, a kinase homology domain, and a guanylyl cyclase catalytic domain. In contrast to other membrane guanylyl cyclases, this enzyme is not activated by natriuretic peptides. Mutations in this gene result in Leber congenital amaurosis and cone-rod dystrophy-6 diseases. [provided by RefSeq, Dec 2008]

GUCY2D links:

(HGNC:):

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 (MetaRNN=0.0038598776).

BP6

Variant 17-8013961-T-A is Benign according to our data. Variant chr17-8013961-T-A is described in ClinVar as [Benign]. Clinvar id is 255475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-8013961-T-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GUCY2D	NM_000180.4 linkuse as main transcript	c.2345T>A	p.Leu782His	missense_variant	12/20	ENST00000254854.5
GUCY2D	XM_011523816.2 linkuse as main transcript	c.2345T>A	p.Leu782His	missense_variant	11/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GUCY2D	ENST00000254854.5 linkuse as main transcript	c.2345T>A	p.Leu782His	missense_variant	12/20	1	NM_000180.4	P1
	ENST00000623126.1 linkuse as main transcript	n.2418A>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.192

AC:

29181

AN:

152088

Hom.:

4029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.167

GnomAD3 exomes

AF:

0.123

AC:

30853

AN:

251294

Hom.:

2799

AF XY:

0.120

AC XY:

16307

AN XY:

135858

show subpopulations

Gnomad AFR exome

AF:

0.404

Gnomad AMR exome

AF:

0.0602

Gnomad ASJ exome

AF:

0.150

Gnomad EAS exome

AF:

0.000707

Gnomad SAS exome

AF:

0.116

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.118

GnomAD4 exome

AF:

0.127

AC:

185391

AN:

1461062

Hom.:

13869

Cov.:

AF XY:

0.126

AC XY:

91788

AN XY:

726852

show subpopulations

Gnomad4 AFR exome

AF:

0.408

Gnomad4 AMR exome

AF:

0.0646

Gnomad4 ASJ exome

AF:

0.149

Gnomad4 EAS exome

AF:

0.000504

Gnomad4 SAS exome

AF:

0.116

Gnomad4 FIN exome

AF:

0.121

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.192

AC:

29245

AN:

152206

Hom.:

4051

Cov.:

AF XY:

0.188

AC XY:

13972

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.399

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.152

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.166

Alfa

AF:

0.131

Hom.:

1172

Bravo

AF:

0.199

TwinsUK

AF:

0.129

AC:

477

ALSPAC

AF:

0.129

AC:

498

ESP6500AA

AF:

0.395

AC:

1740

ESP6500EA

AF:

0.125

AC:

1078

ExAC

AF:

0.130

AC:

15796

Asia WGS

AF:

0.0870

AC:

306

AN:

3478

EpiCase

AF:

0.120

EpiControl

AF:

0.117

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Cone-rod dystrophy 6

Benign:2

Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 10, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Night blindness, congenital stationary, type1i

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Leber congenital amaurosis 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Choroidal dystrophy, central areolar, 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Cone-rod dystrophy 6;C2931258:Leber congenital amaurosis 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 03, 2018

This variant is associated with the following publications: (PMID: 11035546, 17964524, 18161624, 29178642, 17344846, 20079931, 16741161) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.53

Cadd

Benign

Dann

Benign

0.90

DEOGEN2

Benign

0.15

Eigen

Benign

-0.74

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.057

MetaRNN

Benign

0.0039

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.020

MutationTaster

Benign

1.0

PrimateAI

Benign

0.31

PROVEAN

Benign

2.0

REVEL

Benign

0.12

Sift

Benign

0.11

Sift4G

Uncertain

0.058

Polyphen

0.0

Vest4

0.052

MPC

0.28

ClinPred

0.0075

GERP RS

3.1

Varity_R

0.087

gMVP

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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