NM_001079872.2:c.2634G>A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001079872.2(CUL4B):c.2634G>A(p.Arg878Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000682 in 1,195,173 control chromosomes in the GnomAD database, including 4 homozygotes. There are 181 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001079872.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CUL4B | NM_001079872.2 | c.2634G>A | p.Arg878Arg | synonymous_variant | Exon 20 of 20 | ENST00000371322.11 | NP_001073341.1 | |
CUL4B | NM_003588.4 | c.2688G>A | p.Arg896Arg | synonymous_variant | Exon 22 of 22 | NP_003579.3 | ||
CUL4B | NM_001330624.2 | c.2649G>A | p.Arg883Arg | synonymous_variant | Exon 21 of 21 | NP_001317553.1 | ||
CUL4B | NM_001369145.1 | c.2100G>A | p.Arg700Arg | 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.2634G>A | p.Arg878Arg | synonymous_variant | Exon 20 of 20 | 1 | NM_001079872.2 | ENSP00000360373.5 | ||
CUL4B | ENST00000681206.1 | c.2748G>A | p.Arg916Arg | synonymous_variant | Exon 23 of 23 | ENSP00000505480.1 | ||||
CUL4B | ENST00000680673.1 | c.2688G>A | p.Arg896Arg | synonymous_variant | Exon 22 of 22 | ENSP00000505084.1 | ||||
CUL4B | ENST00000681253.1 | c.2688G>A | p.Arg896Arg | synonymous_variant | Exon 23 of 23 | ENSP00000506259.1 | ||||
CUL4B | ENST00000681652.1 | c.2688G>A | p.Arg896Arg | synonymous_variant | Exon 25 of 25 | ENSP00000505176.1 | ||||
CUL4B | ENST00000336592.11 | c.2649G>A | p.Arg883Arg | synonymous_variant | Exon 21 of 21 | 5 | ENSP00000338919.6 | |||
CUL4B | ENST00000674137.11 | c.2640G>A | p.Arg880Arg | synonymous_variant | Exon 20 of 20 | ENSP00000501019.6 | ||||
CUL4B | ENST00000681090.1 | c.2541G>A | p.Arg847Arg | synonymous_variant | Exon 20 of 20 | ENSP00000506288.1 | ||||
CUL4B | ENST00000404115.8 | c.2481G>A | p.Arg827Arg | synonymous_variant | Exon 19 of 19 | 1 | ENSP00000384109.4 | |||
CUL4B | ENST00000679927.1 | c.2289G>A | p.Arg763Arg | synonymous_variant | Exon 21 of 21 | ENSP00000505603.1 | ||||
CUL4B | ENST00000371323.3 | c.2100G>A | p.Arg700Arg | synonymous_variant | Exon 20 of 20 | 5 | ENSP00000360374.3 | |||
CUL4B | ENST00000679844.1 | c.1971G>A | p.Arg657Arg | synonymous_variant | Exon 18 of 18 | ENSP00000505239.1 | ||||
CUL4B | ENST00000680474 | c.*80G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505562.1 | |||||
CUL4B | ENST00000673919.1 | n.*2081G>A | non_coding_transcript_exon_variant | Exon 21 of 21 | ENSP00000500994.1 | |||||
CUL4B | ENST00000674073.2 | n.*190G>A | non_coding_transcript_exon_variant | Exon 18 of 18 | ENSP00000501262.2 | |||||
CUL4B | ENST00000679405.1 | n.*1843G>A | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000504985.1 | |||||
CUL4B | ENST00000679432.1 | n.*1843G>A | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000505343.1 | |||||
CUL4B | ENST00000680918.1 | n.*1550G>A | non_coding_transcript_exon_variant | Exon 18 of 18 | ENSP00000505955.1 | |||||
CUL4B | ENST00000681080.1 | n.*1843G>A | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505898.1 | |||||
CUL4B | ENST00000681189.1 | n.*800G>A | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505973.1 | |||||
CUL4B | ENST00000681333.1 | n.*3527G>A | non_coding_transcript_exon_variant | Exon 17 of 17 | ENSP00000505739.1 | |||||
CUL4B | ENST00000681908.1 | n.*806G>A | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505777.1 | |||||
CUL4B | ENST00000673919.1 | n.*2081G>A | 3_prime_UTR_variant | Exon 21 of 21 | ENSP00000500994.1 | |||||
CUL4B | ENST00000674073.2 | n.*190G>A | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000501262.2 | |||||
CUL4B | ENST00000679405.1 | n.*1843G>A | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000504985.1 | |||||
CUL4B | ENST00000679432.1 | n.*1843G>A | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000505343.1 | |||||
CUL4B | ENST00000680918.1 | n.*1550G>A | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000505955.1 | |||||
CUL4B | ENST00000681080.1 | n.*1843G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505898.1 | |||||
CUL4B | ENST00000681189.1 | n.*800G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505973.1 | |||||
CUL4B | ENST00000681333.1 | n.*3527G>A | 3_prime_UTR_variant | Exon 17 of 17 | ENSP00000505739.1 | |||||
CUL4B | ENST00000681908.1 | n.*806G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505777.1 |
Frequencies
GnomAD3 genomes AF: 0.00357 AC: 399AN: 111724Hom.: 2 Cov.: 23 AF XY: 0.00254 AC XY: 86AN XY: 33920
GnomAD3 exomes AF: 0.000908 AC: 166AN: 182828Hom.: 1 AF XY: 0.000445 AC XY: 30AN XY: 67416
GnomAD4 exome AF: 0.000382 AC: 414AN: 1083397Hom.: 2 Cov.: 26 AF XY: 0.000268 AC XY: 94AN XY: 350503
GnomAD4 genome AF: 0.00359 AC: 401AN: 111776Hom.: 2 Cov.: 23 AF XY: 0.00256 AC XY: 87AN XY: 33982
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
X-linked intellectual disability Cabezas type Benign:1
- -
Inborn genetic diseases Benign:1
This alteration is classified as 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at