chr15-65329021-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004884.4(IGDCC3):c.2333G>A(p.Gly778Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004884.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGDCC3 | NM_004884.4 | c.2333G>A | p.Gly778Asp | missense_variant | Exon 14 of 14 | ENST00000327987.9 | NP_004875.2 | |
IGDCC3 | XM_011522241.3 | c.2330G>A | p.Gly777Asp | missense_variant | Exon 14 of 14 | XP_011520543.3 | ||
IGDCC3 | XM_011522243.1 | c.1964G>A | p.Gly655Asp | missense_variant | Exon 13 of 13 | XP_011520545.1 | ||
IGDCC3 | XM_011522244.2 | c.1922G>A | p.Gly641Asp | missense_variant | Exon 13 of 13 | XP_011520546.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000206 AC: 5AN: 243234Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 132758
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459968Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 726304
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2333G>A (p.G778D) alteration is located in exon 14 (coding exon 14) of the IGDCC3 gene. This alteration results from a G to A substitution at nucleotide position 2333, causing the glycine (G) at amino acid position 778 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