chr16-20333385-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_003361.4(UMOD):c.1862-10T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,458,218 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003361.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UMOD | NM_003361.4 | c.1862-10T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000396138.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UMOD | ENST00000396138.9 | c.1862-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_003361.4 | P2 | |||
UMOD | ENST00000396134.6 | c.1961-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 2 | A2 | ||||
UMOD | ENST00000570689.5 | c.1862-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | P2 | ||||
UMOD | ENST00000570331.1 | n.627-10T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1458218Hom.: 0 Cov.: 30 AF XY: 0.00000966 AC XY: 7AN XY: 724990
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.