7-32869419-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015483.3(KBTBD2):āc.1798A>Gā(p.Thr600Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015483.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KBTBD2 | NM_015483.3 | c.1798A>G | p.Thr600Ala | missense_variant | 4/4 | ENST00000304056.9 | NP_056298.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251240Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135750
GnomAD4 exome AF: 0.0000896 AC: 131AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.0000921 AC XY: 67AN XY: 727230
GnomAD4 genome AF: 0.000105 AC: 16AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.1798A>G (p.T600A) alteration is located in exon 4 (coding exon 3) of the KBTBD2 gene. This alteration results from a A to G substitution at nucleotide position 1798, causing the threonine (T) at amino acid position 600 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at