chr17-65852037-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001199165.4(CEP112):c.2164-3A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,594,824 control chromosomes in the GnomAD database, including 4 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 Likely benign (★).
Frequency
Consequence
NM_001199165.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000710 AC: 108AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000780 AC: 181AN: 232060Hom.: 1 AF XY: 0.000740 AC XY: 93AN XY: 125662
GnomAD4 exome AF: 0.00106 AC: 1535AN: 1442508Hom.: 4 Cov.: 30 AF XY: 0.00104 AC XY: 743AN XY: 717086
GnomAD4 genome AF: 0.000709 AC: 108AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | CEP112: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at