rs748092018
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_032138.7(KBTBD7):āc.1208A>Cā(p.Lys403Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,614,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_032138.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KBTBD7 | ENST00000379483.4 | c.1208A>C | p.Lys403Thr | missense_variant | Exon 1 of 1 | 6 | NM_032138.7 | ENSP00000368797.3 | ||
ENSG00000278390 | ENST00000619407.4 | n.339+30647T>G | intron_variant | Intron 3 of 3 | 2 | |||||
ENSG00000278390 | ENST00000661006.1 | n.245+30647T>G | intron_variant | Intron 2 of 2 | ||||||
ENSG00000278390 | ENST00000615685.4 | n.*215T>G | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152224Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251494Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135920
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000330 AC XY: 24AN XY: 727240
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152224Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74358
ClinVar
Submissions by phenotype
Oromandibular-limb hypogenesis spectrum Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at