Genetic Variant DDAH2:c.-64-385G>A (chr6-31729610-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000375792.7(DDAH2):c.-64-385G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

DDAH2
ENST00000375792.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.795

Publications

49 publications found

Variant links:

Genes affected

DDAH2 (HGNC:2716): (DDAH family member 2, ADMA-independent) This gene encodes a dimethylarginine dimethylaminohydrolase. The encoded enzyme functions in nitric oxide generation by regulating the cellular concentrations of methylarginines, which in turn inhibit nitric oxide synthase activity. The protein may be localized to the mitochondria. Alternative splicing resulting in multiple transcript variants. [provided by RefSeq, Dec 2014]

DDAH2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
DDAH2	NM_013974.3 link	c.-64-385G>A	intron_variant	Intron 1 of 6	NP_039268.1
DDAH2	XM_011514448.3 link	c.-65+73G>A	intron_variant	Intron 1 of 6	XP_011512750.1
DDAH2	NM_001303008.2 link	c.-313G>A	upstream_gene_variant		NP_001289937.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
DDAH2	ENST00000375792.7 link	c.-64-385G>A	intron_variant	Intron 1 of 6	1	ENSP00000364949.3
DDAH2	ENST00000375787.6 link	c.-60-389G>A	intron_variant	Intron 1 of 6	5	ENSP00000364943.2
DDAH2	ENST00000416410.6 link	c.-65+73G>A	intron_variant	Intron 1 of 6	2	ENSP00000397466.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

34392

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

17866

African (AFR)

AF:

0.00

AC:

AN:

976

American (AMR)

AF:

0.00

AC:

AN:

3142

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

990

East Asian (EAS)

AF:

0.00

AC:

AN:

1636

South Asian (SAS)

AF:

0.00

AC:

AN:

3052

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1456

Middle Eastern (MID)

AF:

0.00

AC:

AN:

138

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

21050

Other (OTH)

AF:

0.00

AC:

AN:

1952

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.7

(source)

DANN

Benign

0.88

PhyloP100

0.80

PromoterAI

0.14

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over