Genetic Variant DMAP1:n.979C>G (chr1-44215811-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000488433.5(DMAP1):n.979C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 163,430 control chromosomes in the GnomAD database, including 40,061 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 0.70 ( 37919 hom., cov: 32)

Exomes 𝑓: 0.62 ( 2142 hom. )

Consequence

DMAP1
ENST00000488433.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.214

Publications

2 publications found

Variant links:

Genes affected

DMAP1 (HGNC:18291): (DNA methyltransferase 1 associated protein 1) This gene encodes a subunit of several, distinct complexes involved in the repression or activation of transcription. The encoded protein can independently repress transcription and is targeted to replication foci throughout S phase by interacting directly with the N-terminus of DNA methyltransferase 1. During late S phase, histone deacetylase 2 is added to this complex, providing a means to deacetylate histones in transcriptionally inactive heterochromatin following replication. The encoded protein is also a component of the nucleosome acetyltransferase of H4 complex and interacts with the transcriptional corepressor tumor susceptibility gene 101 and the pro-apoptotic death-associated protein 6, among others. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2008]

DMAP1 links:

ENSG00000302536 (HGNC:):

ENSG00000302536 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
DMAP1	NM_019100.5 link	c.393+913C>G	intron_variant	Intron 3 of 9	ENST00000372289.7	NP_061973.1	Q9NPF5
DMAP1	NM_001034023.2 link	c.393+913C>G	intron_variant	Intron 4 of 10		NP_001029195.1	Q9NPF5
DMAP1	NM_001034024.2 link	c.393+913C>G	intron_variant	Intron 4 of 10		NP_001029196.1	Q9NPF5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMAP1	ENST00000372289.7 link	c.393+913C>G		intron_variant	Intron 3 of 9	1	NM_019100.5	ENSP00000361363.2		Q9NPF5

Frequencies

GnomAD3 genomes

AF:

0.696

AC:

105846

AN:

152020

Hom.:

37847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.872

Gnomad AMI

AF:

0.583

Gnomad AMR

AF:

0.689

Gnomad ASJ

AF:

0.670

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.726

Gnomad FIN

AF:

0.672

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.611

Gnomad OTH

AF:

0.673

GnomAD4 exome

AF:

0.616

AC:

6960

AN:

11292

Hom.:

2142

Cov.:

AF XY:

0.613

AC XY:

3677

AN XY:

5994

show subpopulations

African (AFR)

AF:

0.923

AC:

AN:

American (AMR)

AF:

0.662

AC:

1325

AN:

2002

Ashkenazi Jewish (ASJ)

AF:

0.643

AC:

AN:

112

East Asian (EAS)

AF:

0.446

AC:

173

AN:

388

South Asian (SAS)

AF:

0.689

AC:

951

AN:

1380

European-Finnish (FIN)

AF:

0.659

AC:

145

AN:

220

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.593

AC:

3935

AN:

6636

Other (OTH)

AF:

0.622

AC:

306

AN:

492

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

134

268

403

537

671

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

160

240

320

400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.697

AC:

105981

AN:

152138

Hom.:

37919

Cov.:

AF XY:

0.699

AC XY:

51976

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.872

AC:

36231

AN:

41526

American (AMR)

AF:

0.690

AC:

10543

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.670

AC:

2321

AN:

3466

East Asian (EAS)

AF:

0.501

AC:

2587

AN:

5164

South Asian (SAS)

AF:

0.726

AC:

3497

AN:

4814

European-Finnish (FIN)

AF:

0.672

AC:

7117

AN:

10586

Middle Eastern (MID)

AF:

0.616

AC:

181

AN:

294

European-Non Finnish (NFE)

AF:

0.611

AC:

41545

AN:

67978

Other (OTH)

AF:

0.676

AC:

1430

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1538

3075

4613

6150

7688

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

810

1620

2430

3240

4050

<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:

0.656

Hom.:

4167

Bravo

AF:

0.704

Asia WGS

AF:

0.687

AC:

2389

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

7.8

(source)

DANN

Benign

0.28

PhyloP100

0.21

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over