Genetic Variant NM_033317.5:c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG (chr19-35511468-ACCACTGCTGCCGCCACTGCTGCCG-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM4BA1

The NM_033317.5(DMKN):c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG(p.Gly280_Gly287del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00364 in 1,095,872 control chromosomes in the GnomAD database, including 32 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.016 ( 14 hom., cov: 22)

Exomes 𝑓: 0.0026 ( 18 hom. )

Consequence

DMKN
NM_033317.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.49

Variant links:

Genes affected

DMKN (HGNC:25063): (dermokine) This gene is upregulated in inflammatory diseases, and it was first observed as expressed in the differentiated layers of skin. The most interesting aspect of this gene is the differential use of promoters and terminators to generate isoforms with unique cellular distributions and domain components. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jun 2010]

DMKN links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_033317.5.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMKN	NM_033317.5 link	c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG	p.Gly280_Gly287del	disruptive_inframe_deletion	Exon 5 of 16	ENST00000339686.8	NP_201574.4	Q6E0U4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMKN	ENST00000339686.8 link	c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG	p.Gly280_Gly287del	disruptive_inframe_deletion	Exon 5 of 16	1	NM_033317.5	ENSP00000342012.3		Q6E0U4-1

Frequencies

GnomAD3 genomes

AF:

0.0156

AC:

1311

AN:

84140

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0689

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00739

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.00106

Gnomad SAS

AF:

0.00310

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0337

Gnomad NFE

AF:

0.00135

Gnomad OTH

AF:

0.0103

GnomAD4 exome

AF:

0.00265

AC:

2676

AN:

1011714

Hom.:

AF XY:

0.00252

AC XY:

1258

AN XY:

500112

show subpopulations

Gnomad4 AFR exome

AF:

0.0492

Gnomad4 AMR exome

AF:

0.00865

Gnomad4 ASJ exome

AF:

0.0111

Gnomad4 EAS exome

AF:

0.00299

Gnomad4 SAS exome

AF:

0.00155

Gnomad4 FIN exome

AF:

0.0000643

Gnomad4 NFE exome

AF:

0.00119

Gnomad4 OTH exome

AF:

0.00503

GnomAD4 genome

AF:

0.0156

AC:

1317

AN:

84158

Hom.:

Cov.:

AF XY:

0.0152

AC XY:

623

AN XY:

40924

show subpopulations

Gnomad4 AFR

AF:

0.0691

Gnomad4 AMR

AF:

0.00739

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.00107

Gnomad4 SAS

AF:

0.00312

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00135

Gnomad4 OTH

AF:

0.0101

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over