rs769730471
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001079872.2(CUL4B):c.*7G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000871 in 1,147,536 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001079872.2 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CUL4B | NM_001079872.2 | c.*7G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENST00000371322.11 | NP_001073341.1 | ||
CUL4B | NM_003588.4 | c.*7G>A | 3_prime_UTR_variant | Exon 22 of 22 | NP_003579.3 | |||
CUL4B | NM_001330624.2 | c.*7G>A | 3_prime_UTR_variant | Exon 21 of 21 | NP_001317553.1 | |||
CUL4B | NM_001369145.1 | c.*7G>A | 3_prime_UTR_variant | Exon 20 of 20 | NP_001356074.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CUL4B | ENST00000371322 | c.*7G>A | 3_prime_UTR_variant | Exon 20 of 20 | 1 | NM_001079872.2 | ENSP00000360373.5 | |||
CUL4B | ENST00000681206 | c.*7G>A | 3_prime_UTR_variant | Exon 23 of 23 | ENSP00000505480.1 | |||||
CUL4B | ENST00000680673 | c.*7G>A | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000505084.1 | |||||
CUL4B | ENST00000681253 | c.*7G>A | 3_prime_UTR_variant | Exon 23 of 23 | ENSP00000506259.1 | |||||
CUL4B | ENST00000681652 | c.*7G>A | 3_prime_UTR_variant | Exon 25 of 25 | ENSP00000505176.1 | |||||
CUL4B | ENST00000336592 | c.*7G>A | 3_prime_UTR_variant | Exon 21 of 21 | 5 | ENSP00000338919.6 | ||||
CUL4B | ENST00000674137 | c.*7G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000501019.6 | |||||
CUL4B | ENST00000681090 | c.*7G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000506288.1 | |||||
CUL4B | ENST00000404115 | c.*7G>A | 3_prime_UTR_variant | Exon 19 of 19 | 1 | ENSP00000384109.4 | ||||
CUL4B | ENST00000679927 | c.*7G>A | 3_prime_UTR_variant | Exon 21 of 21 | ENSP00000505603.1 | |||||
CUL4B | ENST00000371323 | c.*7G>A | 3_prime_UTR_variant | Exon 20 of 20 | 5 | ENSP00000360374.3 | ||||
CUL4B | ENST00000680474 | c.*141G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505562.1 | |||||
CUL4B | ENST00000679844 | c.*7G>A | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000505239.1 | |||||
CUL4B | ENST00000673919.1 | n.*2142G>A | non_coding_transcript_exon_variant | Exon 21 of 21 | ENSP00000500994.1 | |||||
CUL4B | ENST00000674073.2 | n.*251G>A | non_coding_transcript_exon_variant | Exon 18 of 18 | ENSP00000501262.2 | |||||
CUL4B | ENST00000679405.1 | n.*1904G>A | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000504985.1 | |||||
CUL4B | ENST00000679432.1 | n.*1904G>A | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000505343.1 | |||||
CUL4B | ENST00000680918.1 | n.*1611G>A | non_coding_transcript_exon_variant | Exon 18 of 18 | ENSP00000505955.1 | |||||
CUL4B | ENST00000681080.1 | n.*1904G>A | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505898.1 | |||||
CUL4B | ENST00000681189.1 | n.*861G>A | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505973.1 | |||||
CUL4B | ENST00000681333.1 | n.*3588G>A | non_coding_transcript_exon_variant | Exon 17 of 17 | ENSP00000505739.1 | |||||
CUL4B | ENST00000681908.1 | n.*867G>A | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505777.1 | |||||
CUL4B | ENST00000673919.1 | n.*2142G>A | 3_prime_UTR_variant | Exon 21 of 21 | ENSP00000500994.1 | |||||
CUL4B | ENST00000674073.2 | n.*251G>A | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000501262.2 | |||||
CUL4B | ENST00000679405.1 | n.*1904G>A | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000504985.1 | |||||
CUL4B | ENST00000679432.1 | n.*1904G>A | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000505343.1 | |||||
CUL4B | ENST00000680918.1 | n.*1611G>A | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000505955.1 | |||||
CUL4B | ENST00000681080.1 | n.*1904G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505898.1 | |||||
CUL4B | ENST00000681189.1 | n.*861G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505973.1 | |||||
CUL4B | ENST00000681333.1 | n.*3588G>A | 3_prime_UTR_variant | Exon 17 of 17 | ENSP00000505739.1 | |||||
CUL4B | ENST00000681908.1 | n.*867G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505777.1 |
Frequencies
GnomAD3 genomes AF: 0.0000535 AC: 6AN: 112073Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34249
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183015Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67561
GnomAD4 exome AF: 0.00000386 AC: 4AN: 1035463Hom.: 0 Cov.: 20 AF XY: 0.00000318 AC XY: 1AN XY: 314813
GnomAD4 genome AF: 0.0000535 AC: 6AN: 112073Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34249
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: CUL4B c.*7G>A is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 1.1e-05 in 183015 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.*7G>A in individuals affected with X-linked intellectual disability Cabezas type and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at