Genetic Variant DCAF4:c.-14G>C (chr14-72926538-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015604.4(DCAF4):c.-14G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,378 control chromosomes in the GnomAD database, including 4,744 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 4744 hom., cov: 33)

Exomes 𝑓: 0.037 ( 0 hom. )

Consequence

DCAF4
NM_015604.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35

Publications

7 publications found

Variant links:

Genes affected

DCAF4 (HGNC:20229): (DDB1 and CUL4 associated factor 4) This gene encodes a WD repeat-containing protein that interacts with the Cul4-Ddb1 E3 ligase macromolecular complex. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2009]

DCAF4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015604.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DCAF4	NM_015604.4	MANE Select	c.-14G>C	5_prime_UTR	Exon 1 of 14	NP_056419.2
DCAF4	NR_147990.2		n.75G>C	non_coding_transcript_exon	Exon 1 of 15
DCAF4	NM_001352449.2		c.-178G>C	5_prime_UTR	Exon 1 of 15	NP_001339378.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DCAF4	ENST00000358377.7	TSL:1 MANE Select	c.-14G>C	5_prime_UTR	Exon 1 of 14	ENSP00000351147.2
DCAF4	ENST00000394234.6	TSL:1	c.-214G>C	5_prime_UTR	Exon 1 of 13	ENSP00000377781.2
DCAF4	ENST00000353777.7	TSL:1	c.-14G>C	5_prime_UTR	Exon 1 of 8	ENSP00000345176.3

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26701

AN:

152126

Hom.:

4731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.457

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.0953

Gnomad ASJ

AF:

0.0596

Gnomad EAS

AF:

0.186

Gnomad SAS

AF:

0.0224

Gnomad FIN

AF:

0.0184

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0644

Gnomad OTH

AF:

0.156

GnomAD4 exome

AF:

0.0373

AC:

AN:

134

Hom.:

Cov.:

AF XY:

0.0510

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0357

AC:

AN:

112

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.176

AC:

26747

AN:

152244

Hom.:

4744

Cov.:

AF XY:

0.169

AC XY:

12545

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.457

AC:

18980

AN:

41514

American (AMR)

AF:

0.0950

AC:

1454

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.0596

AC:

207

AN:

3472

East Asian (EAS)

AF:

0.186

AC:

966

AN:

5182

South Asian (SAS)

AF:

0.0224

AC:

108

AN:

4824

European-Finnish (FIN)

AF:

0.0184

AC:

195

AN:

10616

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0643

AC:

4376

AN:

68010

Other (OTH)

AF:

0.155

AC:

326

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

915

1830

2745

3660

4575

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0151

Hom.:

Bravo

AF:

0.197

Asia WGS

AF:

0.114

AC:

401

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

1.3

(source)

DANN

Benign

0.65

PhyloP100

-1.4

PromoterAI

-0.043

Neutral

(source)

Mutation Taster

=298/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over