11-90202422-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012124.3(CHORDC1):c.982G>T(p.Asp328Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,611,520 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012124.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHORDC1 | NM_012124.3 | c.982G>T | p.Asp328Tyr | missense_variant | Exon 11 of 11 | ENST00000320585.11 | NP_036256.2 | |
CHORDC1 | NM_001144073.2 | c.925G>T | p.Asp309Tyr | missense_variant | Exon 10 of 10 | NP_001137545.1 | ||
CHORDC1 | XM_017017541.3 | c.640G>T | p.Asp214Tyr | missense_variant | Exon 11 of 11 | XP_016873030.1 | ||
CHORDC1 | XM_047426766.1 | c.640G>T | p.Asp214Tyr | missense_variant | Exon 8 of 8 | XP_047282722.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250850Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135568
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459386Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 725994
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.982G>T (p.D328Y) alteration is located in exon 11 (coding exon 11) of the CHORDC1 gene. This alteration results from a G to T substitution at nucleotide position 982, causing the aspartic acid (D) at amino acid position 328 to be replaced by a tyrosine (Y). 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