rs621287

Variant names:

• chr1-85525134-G-A
• rs621287
• ENST00000426972.8:c.-122-28853C>T

Variant summary

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

The NM_001134445.2(DDAH1):​c.-122-28853C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,324 control chromosomes in the GnomAD database, including 1,610 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 0.14 (1610 hom., cov: 27)
• Consequence: DDAH1 NM_001134445.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 3 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]

ENSG00000282057 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134445.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDAH1	NM_001134445.2		c.-122-28853C>T		intron	N/A	NP_001127917.1	O94760-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDAH1	ENST00000426972.8	TSL:1	c.-122-28853C>T		intron	N/A	ENSP00000411189.4	O94760-2
	ENSG00000282057	ENST00000467530.5	TSL:2	n.168-28853C>T		intron	N/A
	ENSG00000282057	ENST00000467666.2	TSL:3	n.276-28853C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21586 AN: 151206 Hom.: 1609 Cov.: 27

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.143 AC: 21592 AN: 151324 Hom.: 1610 Cov.: 27 AF XY: 0.141 AC XY: 10438 AN XY: 73834

African (AFR) AF: 0.104 AC: 4306 AN: 41302

American (AMR) AF: 0.0954 AC: 1447 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3458

East Asian (EAS) AF: 0.110 AC: 569 AN: 5156

South Asian (SAS) AF: 0.208 AC: 980 AN: 4706

European-Finnish (FIN) AF: 0.157 AC: 1636 AN: 10452

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11702 AN: 67778

Other (OTH) AF: 0.119 AC: 250 AN: 2106

Alfa AF: 0.148 Hom.: 158

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.69
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs621287; hg19: chr1-85990817;