X-120560500-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_001079872.2(CUL4B):āc.139A>Gā(p.Ser47Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,208,975 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001079872.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUL4B | NM_001079872.2 | c.139A>G | p.Ser47Gly | missense_variant | 1/20 | ENST00000371322.11 | |
CUL4B | NM_003588.4 | c.193A>G | p.Ser65Gly | missense_variant | 3/22 | ||
CUL4B | NM_001330624.2 | c.154A>G | p.Ser52Gly | missense_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUL4B | ENST00000371322.11 | c.139A>G | p.Ser47Gly | missense_variant | 1/20 | 1 | NM_001079872.2 |
Frequencies
GnomAD3 genomes AF: 0.0000448 AC: 5AN: 111557Hom.: 0 Cov.: 22 AF XY: 0.0000297 AC XY: 1AN XY: 33717
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181916Hom.: 0 AF XY: 0.0000301 AC XY: 2AN XY: 66450
GnomAD4 exome AF: 0.0000264 AC: 29AN: 1097418Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 9AN XY: 362782
GnomAD4 genome AF: 0.0000448 AC: 5AN: 111557Hom.: 0 Cov.: 22 AF XY: 0.0000297 AC XY: 1AN XY: 33717
ClinVar
Submissions by phenotype
X-linked intellectual disability Cabezas type Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at