chr9-78243456-T-G
Variant summary
Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001330691.3(CEP78):c.604-6T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00324 in 1,608,776 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001330691.3 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- cone-rod dystrophy and hearing lossInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, G2P
- cone-rod dystrophy and hearing loss 1Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
- Usher syndrome type 3Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0172 AC: 2621AN: 152188Hom.: 64 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00478 AC: 1167AN: 244158 AF XY: 0.00358 show subpopulations
GnomAD4 exome AF: 0.00178 AC: 2586AN: 1456470Hom.: 68 Cov.: 29 AF XY: 0.00157 AC XY: 1136AN XY: 724526 show subpopulations
GnomAD4 genome AF: 0.0173 AC: 2628AN: 152306Hom.: 64 Cov.: 32 AF XY: 0.0165 AC XY: 1228AN XY: 74476 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
c.604-6T>G in intron 4 of CEP78: This variant is not expected to have clinical s ignificance because it has been identified in 6.45% (629/9758) of African chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs17064247). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at