chr2-58159865-C-T
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000435505.6(VRK2):c.*172C>T variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 1,600,198 control chromosomes in the GnomAD database, including 82,760 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000435505.6 splice_region
Scores
Clinical Significance
Conservation
Publications
- Fanconi anemia complementation group LInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, G2P, Laboratory for Molecular Medicine
- Fanconi anemiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.426 AC: 64600AN: 151798Hom.: 18332 Cov.: 32 show subpopulations
GnomAD4 exome AF: 0.284 AC: 411882AN: 1448282Hom.: 64375 Cov.: 32 AF XY: 0.281 AC XY: 202452AN XY: 719978 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.426 AC: 64720AN: 151916Hom.: 18385 Cov.: 32 AF XY: 0.422 AC XY: 31332AN XY: 74274 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at