dbSNP rs1498374: DDAH1:c.742-83G>A (chr1-85321651-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_012137.4(DDAH1):c.742-83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,056,364 control chromosomes in the GnomAD database, including 18,544 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 0.15 ( 2128 hom., cov: 32)

Exomes 𝑓: 0.19 ( 16416 hom. )

Consequence

DDAH1
NM_012137.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.698

Publications

9 publications found

Variant links:

Genes affected

DDAH1 (HGNC:2715): (dimethylarginine dimethylaminohydrolase 1) This gene belongs to the dimethylarginine dimethylaminohydrolase (DDAH) gene family. The encoded enzyme plays a role in nitric oxide generation by regulating cellular concentrations of methylarginines, which in turn inhibit nitric oxide synthase activity. [provided by RefSeq, Jul 2008]

DDAH1 links:

BCL10-AS1 (HGNC:55868): (BCL10 antisense RNA 1)

BCL10-AS1 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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012137.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DDAH1	NM_012137.4	MANE Select	c.742-83G>A	intron	N/A	NP_036269.1	B2R644
DDAH1	NM_001330655.2		c.442-83G>A	intron	N/A	NP_001317584.1	B4DYP1
DDAH1	NM_001134445.2		c.433-83G>A	intron	N/A	NP_001127917.1	O94760-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DDAH1	ENST00000284031.13	TSL:1 MANE Select	c.742-83G>A	intron	N/A	ENSP00000284031.8	O94760-1
DDAH1	ENST00000426972.8	TSL:1	c.433-83G>A	intron	N/A	ENSP00000411189.4	O94760-2
DDAH1	ENST00000866624.1		c.622-83G>A	intron	N/A	ENSP00000536683.1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22963

AN:

152082

Hom.:

2127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0409

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.217

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.187

AC:

169052

AN:

904164

Hom.:

16416

AF XY:

0.184

AC XY:

86484

AN XY:

469944

show subpopulations

African (AFR)

AF:

0.0364

AC:

808

AN:

22192

American (AMR)

AF:

0.211

AC:

8809

AN:

41744

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

3818

AN:

21380

East Asian (EAS)

AF:

0.104

AC:

3833

AN:

36828

South Asian (SAS)

AF:

0.118

AC:

8446

AN:

71724

European-Finnish (FIN)

AF:

0.226

AC:

11528

AN:

50928

Middle Eastern (MID)

AF:

0.145

AC:

667

AN:

4610

European-Non Finnish (NFE)

AF:

0.202

AC:

123728

AN:

613070

Other (OTH)

AF:

0.178

AC:

7415

AN:

41688

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

6688

13375

20063

26750

33438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3172

6344

9516

12688

15860

<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:

0.151

AC:

22955

AN:

152200

Hom.:

2128

Cov.:

AF XY:

0.151

AC XY:

11262

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0407

AC:

1691

AN:

41550

American (AMR)

AF:

0.213

AC:

3252

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.184

AC:

638

AN:

3468

East Asian (EAS)

AF:

0.140

AC:

726

AN:

5168

South Asian (SAS)

AF:

0.110

AC:

531

AN:

4828

European-Finnish (FIN)

AF:

0.217

AC:

2295

AN:

10590

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.195

AC:

13237

AN:

67984

Other (OTH)

AF:

0.167

AC:

352

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

998

1996

2993

3991

4989

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

244

488

732

976

1220

<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:

0.177

Hom.:

7492

Bravo

AF:

0.147

Asia WGS

AF:

0.102

AC:

354

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.17

(source)

DANN

Benign

0.23

PhyloP100

-0.70

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