Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000180.4(GUCY2D):c.3044-7G>T

CA8366302

255478 (ClinVar)

Gene: GUCY2D
Condition: GUCY2D-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: b5269505-66a7-468f-bd71-2f2fe11a9404
Approved on: 2025-01-30
Published on: 2025-01-30

HGVS expressions

NM_000180.4:c.3044-7G>T
NM_000180.4(GUCY2D):c.3044-7G>T
NC_000017.11:g.8015920G>T
CM000679.2:g.8015920G>T
NC_000017.10:g.7919238G>T
CM000679.1:g.7919238G>T
NC_000017.9:g.7859963G>T
NG_009092.1:g.18251G>T
ENST00000254854.5:c.3044-7G>T
ENST00000254854.4:c.3044-7G>T
NM_000180.3:c.3044-7G>T
More

Benign

Met criteria codes 3
BA1 BS2 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Leber Congenital Amaurosis/early onset Retinal Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GUCY2D Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Leber Congenital Amaurosis/early onset Retinal Dystrophy VCEP
The variant NM_000180.4(GUCY2D):c.3044-7G>T is located in intron 16. This variant is present in gnomAD v.4.1.0 at a Grpmax allele frequency of 0.04452, with 52,788 alleles / 1,177,142 total alleles in the European (non-Finnish) 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 >6 adult individuals in gnomAD (1363 individuals, gnomAD version 4.1.0; BS2). In addition, the splicing impact predictor SpliceAI gives a delta score of 0.04, which is below the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and does not strongly predict an impact on splicing (BP4). 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, BP4. (VCEP specifications version 1.0.0; date of approval 01/22/2025).
Met criteria codes
BA1
This variant is present in gnomAD v.4.1.0 at a Grpmax allele frequency of 0.04452, with 52,788 alleles / 1,177,142 total alleles in the European (non-Finnish) population, which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.016 (BA1).
BS2
This variant has been found in the homozygous state in >6 adult individuals in gnomAD (1363 individuals, gnomAD version 4.1.0; BS2).
BP4
The splicing impact predictor SpliceAI gives a delta score of 0.04, which is below the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and does not strongly predict an impact on splicing (BP4).
Curation History
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