X-120526797-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001079872.2(CUL4B):āc.2652T>Cā(p.Asp884Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000117 in 1,196,164 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001079872.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CUL4B | NM_001079872.2 | c.2652T>C | p.Asp884Asp | synonymous_variant | Exon 20 of 20 | ENST00000371322.11 | NP_001073341.1 | |
CUL4B | NM_003588.4 | c.2706T>C | p.Asp902Asp | synonymous_variant | Exon 22 of 22 | NP_003579.3 | ||
CUL4B | NM_001330624.2 | c.2667T>C | p.Asp889Asp | synonymous_variant | Exon 21 of 21 | NP_001317553.1 | ||
CUL4B | NM_001369145.1 | c.2118T>C | p.Asp706Asp | synonymous_variant | Exon 20 of 20 | NP_001356074.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CUL4B | ENST00000371322.11 | c.2652T>C | p.Asp884Asp | synonymous_variant | Exon 20 of 20 | 1 | NM_001079872.2 | ENSP00000360373.5 | ||
CUL4B | ENST00000681206.1 | c.2766T>C | p.Asp922Asp | synonymous_variant | Exon 23 of 23 | ENSP00000505480.1 | ||||
CUL4B | ENST00000680673.1 | c.2706T>C | p.Asp902Asp | synonymous_variant | Exon 22 of 22 | ENSP00000505084.1 | ||||
CUL4B | ENST00000681253.1 | c.2706T>C | p.Asp902Asp | synonymous_variant | Exon 23 of 23 | ENSP00000506259.1 | ||||
CUL4B | ENST00000681652.1 | c.2706T>C | p.Asp902Asp | synonymous_variant | Exon 25 of 25 | ENSP00000505176.1 | ||||
CUL4B | ENST00000336592.11 | c.2667T>C | p.Asp889Asp | synonymous_variant | Exon 21 of 21 | 5 | ENSP00000338919.6 | |||
CUL4B | ENST00000674137.11 | c.2658T>C | p.Asp886Asp | synonymous_variant | Exon 20 of 20 | ENSP00000501019.6 | ||||
CUL4B | ENST00000681090.1 | c.2559T>C | p.Asp853Asp | synonymous_variant | Exon 20 of 20 | ENSP00000506288.1 | ||||
CUL4B | ENST00000404115.8 | c.2499T>C | p.Asp833Asp | synonymous_variant | Exon 19 of 19 | 1 | ENSP00000384109.4 | |||
CUL4B | ENST00000679927.1 | c.2307T>C | p.Asp769Asp | synonymous_variant | Exon 21 of 21 | ENSP00000505603.1 | ||||
CUL4B | ENST00000371323.3 | c.2118T>C | p.Asp706Asp | synonymous_variant | Exon 20 of 20 | 5 | ENSP00000360374.3 | |||
CUL4B | ENST00000679844.1 | c.1989T>C | p.Asp663Asp | synonymous_variant | Exon 18 of 18 | ENSP00000505239.1 | ||||
CUL4B | ENST00000680474 | c.*98T>C | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505562.1 | |||||
CUL4B | ENST00000673919.1 | n.*2099T>C | non_coding_transcript_exon_variant | Exon 21 of 21 | ENSP00000500994.1 | |||||
CUL4B | ENST00000674073.2 | n.*208T>C | non_coding_transcript_exon_variant | Exon 18 of 18 | ENSP00000501262.2 | |||||
CUL4B | ENST00000679405.1 | n.*1861T>C | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000504985.1 | |||||
CUL4B | ENST00000679432.1 | n.*1861T>C | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000505343.1 | |||||
CUL4B | ENST00000680918.1 | n.*1568T>C | non_coding_transcript_exon_variant | Exon 18 of 18 | ENSP00000505955.1 | |||||
CUL4B | ENST00000681080.1 | n.*1861T>C | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505898.1 | |||||
CUL4B | ENST00000681189.1 | n.*818T>C | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505973.1 | |||||
CUL4B | ENST00000681333.1 | n.*3545T>C | non_coding_transcript_exon_variant | Exon 17 of 17 | ENSP00000505739.1 | |||||
CUL4B | ENST00000681908.1 | n.*824T>C | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505777.1 | |||||
CUL4B | ENST00000673919.1 | n.*2099T>C | 3_prime_UTR_variant | Exon 21 of 21 | ENSP00000500994.1 | |||||
CUL4B | ENST00000674073.2 | n.*208T>C | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000501262.2 | |||||
CUL4B | ENST00000679405.1 | n.*1861T>C | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000504985.1 | |||||
CUL4B | ENST00000679432.1 | n.*1861T>C | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000505343.1 | |||||
CUL4B | ENST00000680918.1 | n.*1568T>C | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000505955.1 | |||||
CUL4B | ENST00000681080.1 | n.*1861T>C | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505898.1 | |||||
CUL4B | ENST00000681189.1 | n.*818T>C | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505973.1 | |||||
CUL4B | ENST00000681333.1 | n.*3545T>C | 3_prime_UTR_variant | Exon 17 of 17 | ENSP00000505739.1 | |||||
CUL4B | ENST00000681908.1 | n.*824T>C | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505777.1 |
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 4AN: 112131Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34261
GnomAD3 exomes AF: 0.0000219 AC: 4AN: 183050Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67578
GnomAD4 exome AF: 0.00000922 AC: 10AN: 1084033Hom.: 0 Cov.: 26 AF XY: 0.00000854 AC XY: 3AN XY: 351195
GnomAD4 genome AF: 0.0000357 AC: 4AN: 112131Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34261
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
CUL4B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at