rs669173

chr1-85433745-T-C

Variant summary

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

The NM_012137.4(DDAH1):c.303+30998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,032 control chromosomes in the GnomAD database, including 13,767 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 0.42 (13767 hom., cov: 32)
• Consequence: DDAH1 NM_012137.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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]

BCL10-AS1 (HGNC:55868): (BCL10 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDAH1	NM_012137.4	c.303+30998A>G		intron_variant		ENST00000284031.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDAH1	ENST00000284031.13	c.303+30998A>G		intron_variant		1	NM_012137.4	P1
DDAH1	ENST00000426972.8	c.-7+62421A>G		intron_variant		1
BCL10-AS1	ENST00000426125.1	n.138-14053T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64253 AN: 151914 Hom.: 13753 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.423 AC: 64310 AN: 152032 Hom.: 13767 Cov.: 32 AF XY: 0.425 AC XY: 31548 AN XY: 74284

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.423

Alfa AF: 0.423 Hom.: 6415

Bravo AF: 0.421

Asia WGS AF: 0.399 AC: 1386 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.46
Dann	Benign	0.51

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: rs669173; hg19: chr1-85899428;