chr10-101064595-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_030929.5(KAZALD1):c.767G>A(p.Arg256His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00183 in 1,613,936 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_030929.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAZALD1 | NM_030929.5 | c.767G>A | p.Arg256His | missense_variant | 4/5 | ENST00000370200.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAZALD1 | ENST00000370200.6 | c.767G>A | p.Arg256His | missense_variant | 4/5 | 1 | NM_030929.5 | P1 | |
KAZALD1 | ENST00000477267.1 | n.282G>A | non_coding_transcript_exon_variant | 3/5 | 5 | ||||
KAZALD1 | ENST00000477979.5 | n.423G>A | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00792 AC: 1205AN: 152212Hom.: 21 Cov.: 33
GnomAD3 exomes AF: 0.00237 AC: 593AN: 250660Hom.: 7 AF XY: 0.00199 AC XY: 270AN XY: 135496
GnomAD4 exome AF: 0.00119 AC: 1745AN: 1461606Hom.: 15 Cov.: 33 AF XY: 0.00113 AC XY: 819AN XY: 727090
GnomAD4 genome ? AF: 0.00794 AC: 1209AN: 152330Hom.: 21 Cov.: 33 AF XY: 0.00753 AC XY: 561AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 25, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at