chrX-23000844-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_182699.4(DDX53):āc.787A>Gā(p.Ile263Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000446 in 1,210,197 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 20 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_182699.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX53 | NM_182699.4 | c.787A>G | p.Ile263Val | missense_variant | 1/1 | ENST00000327968.7 | |
PTCHD1-AS | NR_073010.2 | n.343+63194T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX53 | ENST00000327968.7 | c.787A>G | p.Ile263Val | missense_variant | 1/1 | NM_182699.4 | P1 | ||
ENST00000687248.1 | n.343+63194T>C | intron_variant, non_coding_transcript_variant | |||||||
ENST00000687119.1 | n.83-56696T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 4AN: 112200Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34354
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183154Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67638
GnomAD4 exome AF: 0.0000455 AC: 50AN: 1097997Hom.: 0 Cov.: 32 AF XY: 0.0000523 AC XY: 19AN XY: 363355
GnomAD4 genome AF: 0.0000357 AC: 4AN: 112200Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 24, 2023 | The c.787A>G (p.I263V) alteration is located in exon 1 (coding exon 1) of the DDX53 gene. This alteration results from a A to G substitution at nucleotide position 787, causing the isoleucine (I) at amino acid position 263 to be replaced by a valine (V). 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