4-84635255-T-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001263.4(CDS1):c.723-9T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00233 in 1,297,760 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001263.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDS1 | NM_001263.4 | c.723-9T>A | intron_variant | Intron 7 of 12 | ENST00000295887.6 | NP_001254.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00119 AC: 180AN: 150680Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00394 AC: 705AN: 179016Hom.: 2 AF XY: 0.00452 AC XY: 441AN XY: 97648
GnomAD4 exome AF: 0.00248 AC: 2845AN: 1146974Hom.: 4 Cov.: 18 AF XY: 0.00270 AC XY: 1565AN XY: 580164
GnomAD4 genome AF: 0.00119 AC: 179AN: 150786Hom.: 2 Cov.: 31 AF XY: 0.00144 AC XY: 106AN XY: 73670
ClinVar
Submissions by phenotype
CDS1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at