rs480414

Positions:

• chr1-85461780-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.303+2963C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,040 control chromosomes in the GnomAD database, including 7,639 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 0.31 (7639 hom., cov: 33)
• Consequence: DDAH1 NM_012137.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDAH1	NM_012137.4	c.303+2963C>T		intron_variant		ENST00000284031.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDAH1	ENST00000284031.13	c.303+2963C>T		intron_variant		1	NM_012137.4	P1
DDAH1	ENST00000426972.8	c.-7+34386C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47755 AN: 151922 Hom.: 7630 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.314 AC: 47786 AN: 152040 Hom.: 7639 Cov.: 33 AF XY: 0.313 AC XY: 23276 AN XY: 74320

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.297

Alfa AF: 0.297 Hom.: 11861

Bravo AF: 0.312

Asia WGS AF: 0.331 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.4
DANN	Benign	0.78

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: rs480414; hg19: chr1-85927463;