chr7-122416066-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017954.11(CADPS2):c.2575G>A(p.Ala859Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000722 in 1,523,422 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 Uncertain significance (★).
Frequency
Consequence
NM_017954.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CADPS2 | NM_017954.11 | c.2575G>A | p.Ala859Thr | missense_variant | 18/30 | ENST00000449022.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CADPS2 | ENST00000449022.7 | c.2575G>A | p.Ala859Thr | missense_variant | 18/30 | 5 | NM_017954.11 | ||
ENST00000630777.2 | n.163-23301C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000124 AC: 2AN: 161532Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 85472
GnomAD4 exome AF: 0.00000365 AC: 5AN: 1371228Hom.: 0 Cov.: 28 AF XY: 0.00000148 AC XY: 1AN XY: 673464
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.2596G>A (p.A866T) alteration is located in exon 19 (coding exon 19) of the CADPS2 gene. This alteration results from a G to A substitution at nucleotide position 2596, causing the alanine (A) at amino acid position 866 to be replaced by a threonine (T). 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