chr16-57436730-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020313.4(CIAPIN1):c.313A>G(p.Asn105Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,613,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020313.4 missense, splice_region
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 | UniProt |
---|---|---|---|---|---|---|---|
CIAPIN1 | NM_020313.4 | c.313A>G | p.Asn105Asp | missense_variant, splice_region_variant | 4/9 | ENST00000394391.9 | |
CIAPIN1 | NM_001308347.2 | c.274A>G | p.Asn92Asp | missense_variant, splice_region_variant | 4/9 | ||
CIAPIN1 | NM_001308358.2 | c.313A>G | p.Asn105Asp | missense_variant, splice_region_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIAPIN1 | ENST00000394391.9 | c.313A>G | p.Asn105Asp | missense_variant, splice_region_variant | 4/9 | 1 | NM_020313.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000257 AC: 64AN: 249166Hom.: 0 AF XY: 0.000237 AC XY: 32AN XY: 135228
GnomAD4 exome AF: 0.000141 AC: 206AN: 1460940Hom.: 0 Cov.: 29 AF XY: 0.000147 AC XY: 107AN XY: 726828
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.313A>G (p.N105D) alteration is located in exon 4 (coding exon 3) of the CIAPIN1 gene. This alteration results from a A to G substitution at nucleotide position 313, causing the asparagine (N) at amino acid position 105 to be replaced by an aspartic acid (D). 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