rs1498373

Positions:

• chr1-85324950-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012137.4(DDAH1):​c.598-67C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 1,577,218 control chromosomes in the GnomAD database, including 101,950 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 0.29 (7223 hom., cov: 31)
  • Exomes 𝑓: 0.36 (94727 hom.)
• Consequence: DDAH1 NM_012137.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

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]

BCL10-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDAH1	NM_012137.4	c.598-67C>T		intron_variant		ENST00000284031.13	NP_036269.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDAH1	ENST00000284031.13	c.598-67C>T		intron_variant		1	NM_012137.4	ENSP00000284031.8

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43780 AN: 151876 Hom.: 7225 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.276

GnomAD4 exome AF: 0.361 AC: 513905 AN: 1425226 Hom.: 94727 AF XY: 0.362 AC XY: 255427 AN XY: 706428

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.342

Gnomad4 ASJ exome AF: 0.322

Gnomad4 EAS exome AF: 0.256

Gnomad4 SAS exome AF: 0.407

Gnomad4 FIN exome AF: 0.397

Gnomad4 NFE exome AF: 0.370

Gnomad4 OTH exome AF: 0.338

GnomAD4 genome AF: 0.288 AC: 43771 AN: 151992 Hom.: 7223 Cov.: 31 AF XY: 0.291 AC XY: 21614 AN XY: 74280

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.275

Alfa AF: 0.327 Hom.: 3117

Bravo AF: 0.273

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.8
DANN	Benign	0.59

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

LitVar

Other links and lift over

dbSNP: rs1498373; hg19: chr1-85790633; COSMIC: COSV52302015;