17-8014859-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BS2BA1BP4

This summary comes from the ClinGen Evidence Repository: The NM_000180.4(GUCY2D):c.2577G>T (p.Pro859=) variant is located at the first base of exon 14 and does not alter the amino acid (proline) at position p.859. The splicing impact predictor SpliceAI gives a delta score of 0.03, which is below the ClinGen LCA/eoRD VCEP recommended threshold of <0.1 and does not predict an impact on splicing (BP4). This variant is present in gnomAD v.4.1.0 at a GrpMax allele frequency of 0.04139, with 3871 alleles / 91074 total alleles in the South Asian population, which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.016 (BA1). This variant has been found in the homozygous state in 141 adult individuals in gnomAD which exceeds the LCA/eoRD VCEP threshold of ≥6 (gnomAD version 4.1.0; BS2). In summary, this variant meets the criteria to be classified as Benign for GUCY2D-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: BA1, BS2, BP4. (VCEP specifications version 1.0.0; date of approval 01/22/2025). LINK:https://erepo.genome.network/evrepo/ui/classification/CA201118/MONDO:0100453/167

Frequency

Genomes: 𝑓 0.0059 ( 14 hom., cov: 32)
Exomes 𝑓: 0.0036 ( 127 hom. )

Consequence

GUCY2D
NM_000180.4 splice_region, synonymous

Scores

2
Splicing: ADA: 0.7349
1
1

Clinical Significance

Benign reviewed by expert panel B:6

Conservation

PhyloP100: 0.332
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
For more information check the summary or visit ClinGen Evidence Repository.
BS2
For more information check the summary or visit ClinGen Evidence Repository.
BA1
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GUCY2DNM_000180.4 linkc.2577G>T p.Pro859Pro splice_region_variant, synonymous_variant Exon 14 of 20 ENST00000254854.5 NP_000171.1 Q02846
GUCY2DXM_011523816.2 linkc.2577G>T p.Pro859Pro splice_region_variant, synonymous_variant Exon 13 of 19 XP_011522118.1 Q02846

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GUCY2DENST00000254854.5 linkc.2577G>T p.Pro859Pro splice_region_variant, synonymous_variant Exon 14 of 20 1 NM_000180.4 ENSP00000254854.4 Q02846
ENSG00000279174ENST00000623126.1 linkn.1520C>A non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.00581
AC:
884
AN:
152132
Hom.:
13
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0139
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000981
Gnomad ASJ
AF:
0.00230
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0481
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000588
Gnomad OTH
AF:
0.00574
GnomAD3 exomes
AF:
0.00679
AC:
1707
AN:
251356
Hom.:
45
AF XY:
0.00834
AC XY:
1133
AN XY:
135872
show subpopulations
Gnomad AFR exome
AF:
0.0146
Gnomad AMR exome
AF:
0.000810
Gnomad ASJ exome
AF:
0.00268
Gnomad EAS exome
AF:
0.000163
Gnomad SAS exome
AF:
0.0428
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000634
Gnomad OTH exome
AF:
0.00472
GnomAD4 exome
AF:
0.00360
AC:
5265
AN:
1461852
Hom.:
127
Cov.:
35
AF XY:
0.00470
AC XY:
3420
AN XY:
727228
show subpopulations
Gnomad4 AFR exome
AF:
0.0155
Gnomad4 AMR exome
AF:
0.00105
Gnomad4 ASJ exome
AF:
0.00295
Gnomad4 EAS exome
AF:
0.000126
Gnomad4 SAS exome
AF:
0.0422
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000587
Gnomad4 OTH exome
AF:
0.00517
GnomAD4 genome
AF:
0.00587
AC:
893
AN:
152250
Hom.:
14
Cov.:
32
AF XY:
0.00629
AC XY:
468
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0140
Gnomad4 AMR
AF:
0.000980
Gnomad4 ASJ
AF:
0.00230
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0485
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000588
Gnomad4 OTH
AF:
0.00616
Alfa
AF:
0.00140
Hom.:
0
Bravo
AF:
0.00516
Asia WGS
AF:
0.0310
AC:
109
AN:
3478
EpiCase
AF:
0.000981
EpiControl
AF:
0.000652

ClinVar

Significance: Benign
Submissions summary: Benign:6
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not specified Benign:3
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesApr 28, 2017- -
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 28, 2016Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)May 13, 2015- -
Cone-rod dystrophy 6;C2931258:Leber congenital amaurosis 1 Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 03, 2025- -
GUCY2D-related recessive retinopathy Benign:1
Benign, reviewed by expert panelcurationClinGen Leber Congenital Amaurosis/early Onset Retinal Dystrophy Variant Curation Expert Panel, ClinGenJan 30, 2025The NM_000180.4(GUCY2D):c.2577G>T (p.Pro859=) variant is located at the first base of exon 14 and does not alter the amino acid (proline) at position p.859. The splicing impact predictor SpliceAI gives a delta score of 0.03, which is below the ClinGen LCA/eoRD VCEP recommended threshold of <0.1 and does not predict an impact on splicing (BP4). This variant is present in gnomAD v.4.1.0 at a GrpMax allele frequency of 0.04139, with 3871 alleles / 91074 total alleles in the South Asian population, which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.016 (BA1). This variant has been found in the homozygous state in 141 adult individuals in gnomAD which exceeds the LCA/eoRD VCEP threshold of ≥6 (gnomAD version 4.1.0; BS2). In summary, this variant meets the criteria to be classified as Benign for GUCY2D-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: BA1, BS2, BP4. (VCEP specifications version 1.0.0; date of approval 01/22/2025). -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
13
DANN
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.73
dbscSNV1_RF
Pathogenic
0.82
SpliceAI score (max)
0.030
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.

Other links and lift over

dbSNP: rs112372281; hg19: chr17-7918177; API