12-25108787-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018272.5(DNAI7):c.1930C>T(p.Pro644Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000196 in 866,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018272.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAI7 | NM_018272.5 | c.1930C>T | p.Pro644Ser | missense_variant | 16/16 | ENST00000395987.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAI7 | ENST00000395987.8 | c.1930C>T | p.Pro644Ser | missense_variant | 16/16 | 1 | NM_018272.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000465 AC: 5AN: 107464Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.0000581 AC: 14AN: 241148Hom.: 0 AF XY: 0.0000306 AC XY: 4AN XY: 130808
GnomAD4 exome AF: 0.0000158 AC: 12AN: 759014Hom.: 0 Cov.: 21 AF XY: 0.0000128 AC XY: 5AN XY: 391062
GnomAD4 genome ? AF: 0.0000465 AC: 5AN: 107464Hom.: 0 Cov.: 26 AF XY: 0.0000410 AC XY: 2AN XY: 48756
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2023 | The c.1930C>T (p.P644S) alteration is located in exon 16 (coding exon 16) of the CASC1 gene. This alteration results from a C to T substitution at nucleotide position 1930, causing the proline (P) at amino acid position 644 to be replaced by a serine (S). 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