1-85570890-G-T

Variant names:

• chr1-85570890-G-T
• rs1378228
• ENST00000426972.8:c.-123+7094C>A

Variant summary

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

The ENST00000426972.8(DDAH1):​c.-123+7094C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,836 control chromosomes in the GnomAD database, including 8,336 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 0.32 (8336 hom., cov: 32)
• Consequence: DDAH1 ENST00000426972.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 4 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]

LOC124904208 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426972.8. 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_001134445.2		c.-123+7094C>A		intron	N/A	NP_001127917.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDAH1	ENST00000426972.8	TSL:1	c.-123+7094C>A		intron	N/A	ENSP00000411189.4
	ENSG00000282057	ENST00000467530.5	TSL:2	n.167+7094C>A		intron	N/A
	ENSG00000282057	ENST00000467666.2	TSL:3	n.275+4942C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48957 AN: 151718 Hom.: 8326 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.323 AC: 48991 AN: 151836 Hom.: 8336 Cov.: 32 AF XY: 0.325 AC XY: 24083 AN XY: 74210

African (AFR) AF: 0.246 AC: 10166 AN: 41398

American (AMR) AF: 0.283 AC: 4316 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2493 AN: 5146

South Asian (SAS) AF: 0.602 AC: 2898 AN: 4812

European-Finnish (FIN) AF: 0.278 AC: 2933 AN: 10538

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23594 AN: 67896

Other (OTH) AF: 0.340 AC: 715 AN: 2100

Alfa AF: 0.341 Hom.: 15091

Bravo AF: 0.313

Asia WGS AF: 0.514 AC: 1782 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.55
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1378228; hg19: chr1-86036573;