rs1403955

Positions:

• chr1-85474422-T-G

Variant summary

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

The ENST00000426972.8(DDAH1):​c.-7+21744A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,734 control chromosomes in the GnomAD database, including 11,960 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 0.40 (11960 hom., cov: 31)
• Consequence: DDAH1 ENST00000426972.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDAH1	NM_001134445.2	c.-7+21744A>C		intron_variant
DDAH1	XM_005270707.3	c.18+103562A>C		intron_variant
DDAH1	XM_011541158.2	c.-87+21744A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDAH1	ENST00000426972.8	c.-7+21744A>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60162 AN: 151612 Hom.: 11950 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.397 AC: 60208 AN: 151734 Hom.: 11960 Cov.: 31 AF XY: 0.399 AC XY: 29555 AN XY: 74136

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.380

Alfa AF: 0.399 Hom.: 16848

Bravo AF: 0.390

Asia WGS AF: 0.351 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1403955; hg19: chr1-85940105;