rs11161618

Variant names:

• chr1-85449719-C-T
• rs11161618
• NM_012137.4:c.303+15024G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012137.4(DDAH1):​c.303+15024G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,850 control chromosomes in the GnomAD database, including 10,821 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 0.34 (10821 hom., cov: 31)
• Consequence: DDAH1 NM_012137.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 9 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.479 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDAH1	NM_012137.4	MANE Select	c.303+15024G>A		intron	N/A	NP_036269.1
	DDAH1	NM_001134445.2		c.-7+46447G>A		intron	N/A	NP_001127917.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDAH1	ENST00000284031.13	TSL:1 MANE Select	c.303+15024G>A		intron	N/A	ENSP00000284031.8
	DDAH1	ENST00000426972.8	TSL:1	c.-7+46447G>A		intron	N/A	ENSP00000411189.4

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52311 AN: 151730 Hom.: 10818 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.398

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.345 AC: 52315 AN: 151850 Hom.: 10821 Cov.: 31 AF XY: 0.346 AC XY: 25679 AN XY: 74160

African (AFR) AF: 0.107 AC: 4419 AN: 41454

American (AMR) AF: 0.488 AC: 7443 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1120 AN: 5108

South Asian (SAS) AF: 0.307 AC: 1473 AN: 4794

European-Finnish (FIN) AF: 0.448 AC: 4713 AN: 10524

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.443 AC: 30112 AN: 67944

Other (OTH) AF: 0.396 AC: 838 AN: 2116

Alfa AF: 0.422 Hom.: 25805

Bravo AF: 0.339

Asia WGS AF: 0.256 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.039
DANN	Benign	0.36
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11161618; hg19: chr1-85915402;