12-120446650-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_176818.3(GATC):c.82-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00131 in 1,607,166 control chromosomes in the GnomAD database, including 2 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 Uncertain significance (★).
Frequency
Consequence
NM_176818.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATC | ENST00000551765.6 | c.82-7C>T | splice_region_variant, intron_variant | Intron 1 of 3 | 1 | NM_176818.3 | ENSP00000446872.1 | |||
ENSG00000111780 | ENST00000551806.1 | c.175-7C>T | splice_region_variant, intron_variant | Intron 2 of 4 | 3 | ENSP00000450281.1 | ||||
GATC | ENST00000229384 | c.-157C>T | 5_prime_UTR_variant | Exon 1 of 3 | 2 | ENSP00000229384.5 | ||||
GATC | ENST00000548171.1 | n.82-7C>T | splice_region_variant, intron_variant | Intron 1 of 4 | 2 | ENSP00000448397.1 |
Frequencies
GnomAD3 genomes AF: 0.000788 AC: 120AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000663 AC: 163AN: 245814Hom.: 0 AF XY: 0.000607 AC XY: 81AN XY: 133364
GnomAD4 exome AF: 0.00136 AC: 1981AN: 1454796Hom.: 2 Cov.: 33 AF XY: 0.00134 AC XY: 967AN XY: 722882
GnomAD4 genome AF: 0.000794 AC: 121AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.000698 AC XY: 52AN XY: 74516
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation deficiency 42 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at