chrX-2488954-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001171136.2(ZBED1):āc.1766A>Gā(p.Lys589Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000943 in 1,597,150 control chromosomes in the GnomAD database, including 12 homozygotes. There are 647 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Benignin ClinVar.
Frequency
Consequence
NM_001171136.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBED1 | NM_001171136.2 | c.1766A>G | p.Lys589Arg | missense_variant | 2/2 | ENST00000652001.1 | |
DHRSX | NM_145177.3 | c.109+11863A>G | intron_variant | ENST00000334651.11 | |||
ZBED1 | NM_001171135.2 | c.1766A>G | p.Lys589Arg | missense_variant | 2/2 | ||
ZBED1 | NM_004729.4 | c.1766A>G | p.Lys589Arg | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBED1 | ENST00000652001.1 | c.1766A>G | p.Lys589Arg | missense_variant | 2/2 | NM_001171136.2 | P1 | ||
DHRSX | ENST00000334651.11 | c.109+11863A>G | intron_variant | 1 | NM_145177.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00523 AC: 796AN: 152132Hom.: 6 Cov.: 33 AF XY: 0.00487 AC XY: 362AN XY: 74306
GnomAD3 exomes AF: 0.00153 AC: 364AN: 237392Hom.: 3 AF XY: 0.00110 AC XY: 140AN XY: 127268
GnomAD4 exome AF: 0.000489 AC: 706AN: 1444900Hom.: 6 Cov.: 31 AF XY: 0.000392 AC XY: 281AN XY: 716540
GnomAD4 genome AF: 0.00525 AC: 800AN: 152250Hom.: 6 Cov.: 33 AF XY: 0.00492 AC XY: 366AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at