Genetic Variant DCPH1:c.559-123T>G (chr6-151468220-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024573.3(DCPH1):c.559-123T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 620,922 control chromosomes in the GnomAD database, including 75,907 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 0.54 ( 25057 hom., cov: 33)

Exomes 𝑓: 0.45 ( 50850 hom. )

Consequence

DCPH1
NM_024573.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0800

Publications

11 publications found

Variant links:

Genes affected

DCPH1 (HGNC:17872): (acidic residue methyltransferase 1) Enables S-adenosylmethionine-dependent methyltransferase activity; enzyme binding activity; and protein carboxyl O-methyltransferase activity. Involved in methylation and regulation of response to DNA damage stimulus. [provided by Alliance of Genome Resources, Apr 2022]

DCPH1 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024573.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCPH1	NM_024573.3	MANE Select	c.559-123T>G		intron	N/A	NP_078849.1	Q9H993
	DCPH1	NM_001286562.2		c.202-123T>G		intron	N/A	NP_001273491.1	F5GZY1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARMT1	ENST00000367294.4	TSL:1 MANE Select	c.559-123T>G	intron	N/A	ENSP00000356263.3	Q9H993
ARMT1	ENST00000852535.1		c.559-93T>G	intron	N/A	ENSP00000522594.1
ARMT1	ENST00000852534.1		c.565-123T>G	intron	N/A	ENSP00000522593.1

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82360

AN:

151990

Hom.:

25003

Cov.:

show subpopulations

Gnomad AFR

AF:

0.822

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.472

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.767

Gnomad SAS

AF:

0.533

Gnomad FIN

AF:

0.396

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.401

Gnomad OTH

AF:

0.529

GnomAD4 exome

AF:

0.451

AC:

211475

AN:

468814

Hom.:

50850

AF XY:

0.452

AC XY:

111735

AN XY:

246962

show subpopulations

African (AFR)

AF:

0.820

AC:

10506

AN:

12816

American (AMR)

AF:

0.450

AC:

7531

AN:

16744

Ashkenazi Jewish (ASJ)

AF:

0.452

AC:

6213

AN:

13740

East Asian (EAS)

AF:

0.704

AC:

22201

AN:

31544

South Asian (SAS)

AF:

0.530

AC:

20961

AN:

39532

European-Finnish (FIN)

AF:

0.392

AC:

12938

AN:

32978

Middle Eastern (MID)

AF:

0.522

AC:

1035

AN:

1984

European-Non Finnish (NFE)

AF:

0.401

AC:

117580

AN:

293070

Other (OTH)

AF:

0.474

AC:

12510

AN:

26406

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

5489

10978

16466

21955

27444

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1162

2324

3486

4648

5810

<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:

0.542

AC:

82467

AN:

152108

Hom.:

25057

Cov.:

AF XY:

0.544

AC XY:

40450

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.822

AC:

34108

AN:

41500

American (AMR)

AF:

0.472

AC:

7209

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1593

AN:

3472

East Asian (EAS)

AF:

0.766

AC:

3969

AN:

5182

South Asian (SAS)

AF:

0.533

AC:

2572

AN:

4826

European-Finnish (FIN)

AF:

0.396

AC:

4175

AN:

10552

Middle Eastern (MID)

AF:

0.527

AC:

155

AN:

294

European-Non Finnish (NFE)

AF:

0.401

AC:

27231

AN:

67976

Other (OTH)

AF:

0.534

AC:

1128

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1694

3388

5082

6776

8470

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

688

1376

2064

2752

3440

<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:

0.447

Hom.:

8663

Bravo

AF:

0.560

Asia WGS

AF:

0.657

AC:

2273

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.4

(source)

DANN

Benign

0.66

PhyloP100

0.080

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over