X-2490618-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001171136.2(ZBED1):c.102C>T(p.Asn34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000571 in 1,613,980 control chromosomes in the GnomAD database, including 3 homozygotes. There are 394 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. N34N) has been classified as Benign.
Frequency
Consequence
NM_001171136.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBED1 | NM_001171136.2 | c.102C>T | p.Asn34= | synonymous_variant | 2/2 | ENST00000652001.1 | |
DHRSX | NM_145177.3 | c.109+10199C>T | intron_variant | ENST00000334651.11 | |||
ZBED1 | NM_001171135.2 | c.102C>T | p.Asn34= | synonymous_variant | 2/2 | ||
ZBED1 | NM_004729.4 | c.102C>T | p.Asn34= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBED1 | ENST00000652001.1 | c.102C>T | p.Asn34= | synonymous_variant | 2/2 | NM_001171136.2 | P1 | ||
DHRSX | ENST00000334651.11 | c.109+10199C>T | intron_variant | 1 | NM_145177.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00308 AC: 468AN: 152190Hom.: 1 Cov.: 32 AF XY: 0.00273 AC XY: 203AN XY: 74344
GnomAD3 exomes AF: 0.000784 AC: 197AN: 251180Hom.: 1 AF XY: 0.000582 AC XY: 79AN XY: 135742
GnomAD4 exome AF: 0.000309 AC: 451AN: 1461672Hom.: 2 Cov.: 33 AF XY: 0.000263 AC XY: 191AN XY: 727146
GnomAD4 genome AF: 0.00309 AC: 470AN: 152308Hom.: 1 Cov.: 32 AF XY: 0.00273 AC XY: 203AN XY: 74472
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