chr16-58708301-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002080.4(GOT2):c.1171-8C>G 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 0.00171 in 1,613,344 control chromosomes in the GnomAD database, including 17 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 Benign (★).
Frequency
Consequence
NM_002080.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOT2 | NM_002080.4 | c.1171-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000245206.10 | |||
GOT2 | NM_001286220.2 | c.1042-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOT2 | ENST00000245206.10 | c.1171-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002080.4 | P1 | |||
GOT2 | ENST00000434819.2 | c.1042-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00192 AC: 292AN: 152244Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00177 AC: 441AN: 249654Hom.: 0 AF XY: 0.00179 AC XY: 241AN XY: 134986
GnomAD4 exome AF: 0.00168 AC: 2459AN: 1460982Hom.: 13 Cov.: 30 AF XY: 0.00168 AC XY: 1221AN XY: 726804
GnomAD4 genome AF: 0.00192 AC: 292AN: 152362Hom.: 4 Cov.: 33 AF XY: 0.00251 AC XY: 187AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at