X-2489886-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001171136.2(ZBED1):c.834G>A(p.Ala278=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00327 in 1,613,834 control chromosomes in the GnomAD database, including 138 homozygotes. There are 2,311 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. A278A) 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBED1 | NM_001171136.2 | c.834G>A | p.Ala278= | synonymous_variant | 2/2 | ENST00000652001.1 | |
DHRSX | NM_145177.3 | c.109+10931G>A | intron_variant | ENST00000334651.11 | |||
ZBED1 | NM_001171135.2 | c.834G>A | p.Ala278= | synonymous_variant | 2/2 | ||
ZBED1 | NM_004729.4 | c.834G>A | p.Ala278= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBED1 | ENST00000652001.1 | c.834G>A | p.Ala278= | synonymous_variant | 2/2 | NM_001171136.2 | P1 | ||
DHRSX | ENST00000334651.11 | c.109+10931G>A | intron_variant | 1 | NM_145177.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0174 AC: 2644AN: 152222Hom.: 83 Cov.: 33 AF XY: 0.0166 AC XY: 1232AN XY: 74362
GnomAD3 exomes AF: 0.00473 AC: 1187AN: 251066Hom.: 32 AF XY: 0.00336 AC XY: 456AN XY: 135734
GnomAD4 exome AF: 0.00180 AC: 2624AN: 1461494Hom.: 55 Cov.: 31 AF XY: 0.00148 AC XY: 1074AN XY: 727066
GnomAD4 genome AF: 0.0174 AC: 2651AN: 152340Hom.: 83 Cov.: 33 AF XY: 0.0166 AC XY: 1237AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at