chr12-122208497-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001371333.1(DIABLO):c.604C>T(p.Arg202Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R202Q) has been classified as Likely benign.
Frequency
Consequence
NM_001371333.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIABLO | NM_001371333.1 | c.604C>T | p.Arg202Trp | missense_variant | 6/6 | ENST00000464942.7 | |
B3GNT4 | NM_030765.4 | c.*1109G>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.604C>T | p.Arg202Trp | missense_variant | 6/6 | 1 | NM_001371333.1 | P1 | |
B3GNT4 | ENST00000324189.5 | c.*1109G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_030765.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251274Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135832
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727198
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74326
ClinVar
Submissions by phenotype
DIABLO-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 03, 2023 | The DIABLO c.604C>T variant is predicted to result in the amino acid substitution p.Arg202Trp. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.018% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/12-122693044-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at