X-11118490-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_005333.5(HCCS):c.402-11T>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 0.0000721 in 1,192,183 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005333.5 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 |
---|---|---|---|---|---|---|---|
HCCS | NM_005333.5 | c.402-11T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000380762.5 | |||
HCCS | NM_001122608.3 | c.402-11T>C | splice_polypyrimidine_tract_variant, intron_variant | ||||
HCCS | NM_001171991.3 | c.402-11T>C | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCCS | ENST00000380762.5 | c.402-11T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005333.5 | P1 | |||
HCCS | ENST00000380763.7 | c.402-11T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
HCCS | ENST00000321143.8 | c.402-11T>C | splice_polypyrimidine_tract_variant, intron_variant | 2 | P1 | ||||
ARHGAP6 | ENST00000657361.1 | c.1784-131A>G | intron_variant | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000536 AC: 6AN: 112033Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34187
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183277Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67813
GnomAD4 exome AF: 0.0000741 AC: 80AN: 1080150Hom.: 0 Cov.: 26 AF XY: 0.0000460 AC XY: 16AN XY: 347678
GnomAD4 genome ? AF: 0.0000536 AC: 6AN: 112033Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34187
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at