chr7-134933628-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_033138.4(CALD1):āc.859A>Cā(p.Lys287Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00028 in 1,611,560 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_033138.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALD1 | NM_033138.4 | c.859A>C | p.Lys287Gln | missense_variant | 5/15 | ENST00000361675.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALD1 | ENST00000361675.7 | c.859A>C | p.Lys287Gln | missense_variant | 5/15 | 1 | NM_033138.4 | ||
ENST00000665703.1 | n.71+64455T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152188Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000185 AC: 45AN: 242712Hom.: 0 AF XY: 0.000168 AC XY: 22AN XY: 131188
GnomAD4 exome AF: 0.000284 AC: 415AN: 1459254Hom.: 0 Cov.: 33 AF XY: 0.000284 AC XY: 206AN XY: 725474
GnomAD4 genome AF: 0.000236 AC: 36AN: 152306Hom.: 0 Cov.: 30 AF XY: 0.000215 AC XY: 16AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.859A>C (p.K287Q) alteration is located in exon 5 (coding exon 3) of the CALD1 gene. This alteration results from a A to C substitution at nucleotide position 859, causing the lysine (K) at amino acid position 287 to be replaced by a glutamine (Q). 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