15-65328917-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004884.4(IGDCC3):c.2437G>C(p.Glu813Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000786 in 1,539,612 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_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.2437G>C | p.Glu813Gln | missense_variant | Exon 14 of 14 | ENST00000327987.9 | NP_004875.2 | |
IGDCC3 | XM_011522241.3 | c.2434G>C | p.Glu812Gln | missense_variant | Exon 14 of 14 | XP_011520543.3 | ||
IGDCC3 | XM_011522243.1 | c.2068G>C | p.Glu690Gln | missense_variant | Exon 13 of 13 | XP_011520545.1 | ||
IGDCC3 | XM_011522244.2 | c.2026G>C | p.Glu676Gln | missense_variant | Exon 13 of 13 | XP_011520546.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000432 AC: 8AN: 185054Hom.: 0 AF XY: 0.0000401 AC XY: 4AN XY: 99646
GnomAD4 exome AF: 0.0000836 AC: 116AN: 1387362Hom.: 0 Cov.: 30 AF XY: 0.0000906 AC XY: 62AN XY: 684156
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2437G>C (p.E813Q) alteration is located in exon 14 (coding exon 14) of the IGDCC3 gene. This alteration results from a G to C substitution at nucleotide position 2437, causing the glutamic acid (E) at amino acid position 813 to be replaced by a glutamine (Q). 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