chr3-51420750-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001387579.1(DCAF1):​c.2220C>T​(p.Ser740Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0049 in 1,614,044 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0045 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0049 ( 32 hom. )

Consequence

DCAF1
NM_001387579.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.942
Variant links:
Genes affected
DCAF1 (HGNC:30911): (DDB1 and CUL4 associated factor 1) Enables estrogen receptor binding activity and histone kinase activity (H2A-T120 specific). Involved in cell competition in a multicellular organism; histone H2A-T120 phosphorylation; and negative regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. Part of Cul4-RING E3 ubiquitin ligase complex. Colocalizes with COP9 signalosome. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 3-51420750-G-A is Benign according to our data. Variant chr3-51420750-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2653872.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.942 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DCAF1NM_001387579.1 linkuse as main transcriptc.2220C>T p.Ser740Ser synonymous_variant 15/25 ENST00000684031.1 NP_001374508.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DCAF1ENST00000684031.1 linkuse as main transcriptc.2220C>T p.Ser740Ser synonymous_variant 15/25 NM_001387579.1 ENSP00000506880.1 Q9Y4B6-1
DCAF1ENST00000504652.5 linkuse as main transcriptc.2217C>T p.Ser739Ser synonymous_variant 14/251 ENSP00000421724.2 Q9Y4B6-2
DCAF1ENST00000423656.5 linkuse as main transcriptc.2220C>T p.Ser740Ser synonymous_variant 14/255 ENSP00000393183.2 Q9Y4B6-1

Frequencies

GnomAD3 genomes
AF:
0.00449
AC:
683
AN:
152218
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00109
Gnomad AMI
AF:
0.00329
Gnomad AMR
AF:
0.00681
Gnomad ASJ
AF:
0.00605
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00132
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00704
Gnomad OTH
AF:
0.00717
GnomAD3 exomes
AF:
0.00438
AC:
1092
AN:
249270
Hom.:
13
AF XY:
0.00449
AC XY:
607
AN XY:
135230
show subpopulations
Gnomad AFR exome
AF:
0.000710
Gnomad AMR exome
AF:
0.00272
Gnomad ASJ exome
AF:
0.00646
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000752
Gnomad FIN exome
AF:
0.00316
Gnomad NFE exome
AF:
0.00709
Gnomad OTH exome
AF:
0.00496
GnomAD4 exome
AF:
0.00495
AC:
7231
AN:
1461708
Hom.:
32
Cov.:
32
AF XY:
0.00491
AC XY:
3570
AN XY:
727136
show subpopulations
Gnomad4 AFR exome
AF:
0.000717
Gnomad4 AMR exome
AF:
0.00329
Gnomad4 ASJ exome
AF:
0.00647
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000603
Gnomad4 FIN exome
AF:
0.00339
Gnomad4 NFE exome
AF:
0.00568
Gnomad4 OTH exome
AF:
0.00495
GnomAD4 genome
AF:
0.00448
AC:
682
AN:
152336
Hom.:
2
Cov.:
32
AF XY:
0.00408
AC XY:
304
AN XY:
74504
show subpopulations
Gnomad4 AFR
AF:
0.00108
Gnomad4 AMR
AF:
0.00680
Gnomad4 ASJ
AF:
0.00605
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00132
Gnomad4 NFE
AF:
0.00703
Gnomad4 OTH
AF:
0.00710
Alfa
AF:
0.00592
Hom.:
0
Bravo
AF:
0.00476
EpiCase
AF:
0.00632
EpiControl
AF:
0.00800

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2022DCAF1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
3.9
DANN
Benign
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs150385433; hg19: chr3-51458204; API