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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCPH1	NM_024573.3 link	c.559-123T>G		intron_variant	Intron 4 of 4	ENST00000367294.4	NP_078849.1
DCPH1	NM_001286562.2 link	c.202-123T>G		intron_variant	Intron 3 of 3		NP_001273491.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ARMT1	ENST00000367294.4 link	c.559-123T>G	intron_variant	Intron 4 of 4	1	NM_024573.3	ENSP00000356263.3
ARMT1	ENST00000545879.5 link	c.202-123T>G	intron_variant	Intron 3 of 3	2		ENSP00000444121.1
ARMT1	ENST00000494826.1 link	n.*282-123T>G	intron_variant	Intron 3 of 3	2		ENSP00000435882.1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over