2-219172744-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015680.6(CNPPD1):c.1075G>A(p.Val359Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,612,296 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 (★).
Frequency
Consequence
NM_015680.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNPPD1 | NM_015680.6 | c.1075G>A | p.Val359Ile | missense_variant | 8/8 | ENST00000360507.10 | NP_056495.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNPPD1 | ENST00000360507.10 | c.1075G>A | p.Val359Ile | missense_variant | 8/8 | 1 | NM_015680.6 | ENSP00000353698 | P1 | |
CNPPD1 | ENST00000409789.5 | c.1075G>A | p.Val359Ile | missense_variant | 9/9 | 1 | ENSP00000386277 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 151978Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248146Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134144
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460318Hom.: 0 Cov.: 59 AF XY: 0.00000138 AC XY: 1AN XY: 726386
GnomAD4 genome AF: 0.0000855 AC: 13AN: 151978Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74208
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2024 | The c.1075G>A (p.V359I) alteration is located in exon 8 (coding exon 8) of the CNPPD1 gene. This alteration results from a G to A substitution at nucleotide position 1075, causing the valine (V) at amino acid position 359 to be replaced by an isoleucine (I). 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