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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KBTBD7 | NM_032138.7 | c.1208A>C | p.Lys403Thr | missense_variant | 1/1 | ENST00000379483.4 | |
LOC101929140 | NR_120423.1 | n.350+30647T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KBTBD7 | ENST00000379483.4 | c.1208A>C | p.Lys403Thr | missense_variant | 1/1 | NM_032138.7 | P1 | ||
KBTBD6-DT | ENST00000619407.4 | n.339+30647T>G | intron_variant, non_coding_transcript_variant | 2 | |||||
KBTBD6-DT | ENST00000661006.1 | n.245+30647T>G | intron_variant, non_coding_transcript_variant |
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
Likely benign, no assertion criteria provided | research | CHU Sainte-Justine Research Center, University of Montreal | Aug 12, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at