chr2-99069003-GA-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_025244.4(TSGA10):c.1108-6del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,395,340 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_025244.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSGA10 | NM_025244.4 | c.1108-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000393483.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSGA10 | ENST00000393483.8 | c.1108-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_025244.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000199 AC: 3AN: 151060Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000310 AC: 5AN: 161198Hom.: 0 AF XY: 0.0000334 AC XY: 3AN XY: 89916
GnomAD4 exome AF: 0.00000884 AC: 11AN: 1244162Hom.: 0 Cov.: 20 AF XY: 0.00000974 AC XY: 6AN XY: 616020
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151178Hom.: 0 Cov.: 32 AF XY: 0.0000406 AC XY: 3AN XY: 73810
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | TSGA10: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at