chr1-167950253-G-C

Variant names:

• chr1-167950253-G-C
• rs202274
• NM_001198956.2:c.98-1547G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001198956.2(DCAF6):​c.98-1547G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,978 control chromosomes in the GnomAD database, including 3,730 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 (3730 hom., cov: 33)
• Consequence: DCAF6 NM_001198956.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 0 publications found

Genes affected

DCAF6 (HGNC:30002): (DDB1 and CUL4 associated factor 6) The protein encoded by this gene is a ligand-dependent coactivator of nuclear receptors, including nuclear receptor subfamily 3 group C member 1 (NR3C1), glucocorticoid receptor (GR), and androgen receptor (AR). The encoded protein and DNA damage binding protein 2 (DDB2) may act as tumor promoters and tumor suppressors, respectively, by regulating the level of androgen receptor in prostate tissues. In addition, this protein can act with glucocorticoid receptor to promote human papillomavirus gene expression. [provided by RefSeq, Mar 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001198956.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCAF6	NM_001198956.2	MANE Select	c.98-1547G>C		intron	N/A	NP_001185885.1
	DCAF6	NM_001349773.2		c.98-1547G>C		intron	N/A	NP_001336702.1
	DCAF6	NM_001198957.2		c.98-1547G>C		intron	N/A	NP_001185886.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCAF6	ENST00000367840.4	TSL:1 MANE Select	c.98-1547G>C		intron	N/A	ENSP00000356814.3
	DCAF6	ENST00000312263.10	TSL:1	c.98-1547G>C		intron	N/A	ENSP00000311949.6
	DCAF6	ENST00000432587.6	TSL:2	c.98-1547G>C		intron	N/A	ENSP00000396238.2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27523 AN: 151858 Hom.: 3716 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0594

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.151

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.181 AC: 27573 AN: 151978 Hom.: 3730 Cov.: 33 AF XY: 0.181 AC XY: 13469 AN XY: 74266

African (AFR) AF: 0.378 AC: 15672 AN: 41436

American (AMR) AF: 0.132 AC: 2023 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3466

East Asian (EAS) AF: 0.0585 AC: 303 AN: 5176

South Asian (SAS) AF: 0.0702 AC: 338 AN: 4816

European-Finnish (FIN) AF: 0.161 AC: 1694 AN: 10512

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0984 AC: 6686 AN: 67980

Other (OTH) AF: 0.149 AC: 315 AN: 2110

Alfa AF: 0.0491 Hom.: 46

Bravo AF: 0.186

Asia WGS AF: 0.0790 AC: 274 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.32
DANN	Benign	0.54
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs202274; hg19: chr1-167919491;