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 label mismatch: RS1 vs undefined
  • 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_000330.4(RS1):c.576C>T (p.Pro192=)

CA10360603

255840 (ClinVar)

Gene: RS1
Condition: X-linked retinoschisis
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 8df73444-cd98-483e-9315-d1897b75ef2d
Approved on: 2025-05-19
Published on: 2025-05-20

HGVS expressions

NM_000330.4:c.576C>T
NM_000330.4(RS1):c.576C>T (p.Pro192=)
NC_000023.11:g.18642103G>A
CM000685.2:g.18642103G>A
NC_000023.10:g.18660223G>A
CM000685.1:g.18660223G>A
NC_000023.9:g.18570144G>A
NG_008475.1:g.221499G>A
NG_008659.3:g.40346C>T
ENST00000379984.4:c.576C>T
ENST00000379984.3:c.576C>T
ENST00000379989.6:c.2714-3904G>A
ENST00000379996.7:c.2714-3904G>A
ENST00000476595.1:n.1067C>T
NM_000330.3:c.576C>T
NM_001037343.1:c.2714-3904G>A
NM_003159.2:c.2714-3904G>A
NM_001037343.2:c.2714-3904G>A
NM_003159.3:c.2714-3904G>A
More

Benign

Met criteria codes 3
BA1 BP7 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RS1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
X-linked Inherited Retinal Disease VCEP
The NM_000330.4(RS1):c.576C>T variant is a synonymous variant at codon 192. This variant is present in gnomAD v.4.1.0 at a frequency of 0.0003976 among hemizygous individuals, with 158 variant alleles / 397377 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.0002 (BA1). The splicing impact predictor SpliceAI gives a delta score of 0.00 for all delta-type changes, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP4). This silent variant causing a synonymous variant at codon 192 does not have an impact at splicing sites according to Splice AI, which predicts a delta score of 0.00 for all delta-type changes which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP7). In summary, this variant is classified as benign for X-linked retinoschisis based on the ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RS1 Version 1.0.0: BA1, BP4, and BP7 (date of approval 01/24/2025).
Met criteria codes
BA1
This variant is present in gnomAD v.4.1.0 at a frequency of 0.0003976 among hemizygous individuals, with 158 variant alleles / 397377 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.0002 (BA1).
BP7
This silent variant causing a synonymous variant at codon 192 does not have an impact at splicing sites according to Splice AI, which predicts a delta score of 0.00 for all delta-type changes which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP7).
BP4
The splicing impact predictor SpliceAI gives a delta score of 0.00 for all delta type changes, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP4).
Curation History
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