rs10782551

chr1-85473592-G-Achr1-85473592-G-T

Variant summary

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

The ENST00000426972.8(DDAH1):c.-7+22574C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0798 in 151,700 control chromosomes in the GnomAD database, including 562 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 0.080 (562 hom., cov: 32)
• Consequence: DDAH1 ENST00000426972.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDAH1	NM_001134445.2	c.-7+22574C>T		intron_variant
DDAH1	XM_005270707.3	c.18+104392C>T		intron_variant
DDAH1	XM_011541158.2	c.-87+22574C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDAH1	ENST00000426972.8	c.-7+22574C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0798 AC: 12094 AN: 151582 Hom.: 560 Cov.: 32

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0798 AC: 12101 AN: 151700 Hom.: 562 Cov.: 32 AF XY: 0.0830 AC XY: 6153 AN XY: 74130

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.0463

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0624

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0576 Hom.: 314

Bravo AF: 0.0761

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.5
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10782551; hg19: chr1-85939275;