chr12-122208576-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The ENST00000267169.11(DIABLO):c.611C>T(p.Ala204Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,611,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/11 in silico tools predict 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 Likely benign (★).
Frequency
Consequence
ENST00000267169.11 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIABLO | NM_001371333.1 | c.525C>T | p.Gly175= | splice_region_variant, synonymous_variant | 6/6 | ENST00000464942.7 | |
B3GNT4 | NM_030765.4 | c.*1188G>A | 3_prime_UTR_variant | 3/3 | ENST00000324189.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIABLO | ENST00000464942.7 | c.525C>T | p.Gly175= | splice_region_variant, synonymous_variant | 6/6 | 1 | NM_001371333.1 | P1 | |
B3GNT4 | ENST00000324189.5 | c.*1188G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_030765.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249086Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134992
GnomAD4 exome AF: 0.0000480 AC: 70AN: 1459534Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 726242
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 20, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at