rs233112

Positions:

• chr1-85320068-T-C
• chr1-85320068-T-G

Variant summary

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

The NM_012137.4(DDAH1):​c.*1384A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,076 control chromosomes in the GnomAD database, including 10,288 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 0.37 (10287 hom., cov: 32)
  • Exomes 𝑓: 0.38 (1 hom.)
• Consequence: DDAH1 NM_012137.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDAH1	NM_012137.4	c.*1384A>G		3_prime_UTR_variant	6/6	ENST00000284031.13	NP_036269.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDAH1	ENST00000284031.13	c.*1384A>G		3_prime_UTR_variant	6/6	1	NM_012137.4	ENSP00000284031.8

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55598 AN: 151950 Hom.: 10280 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.366 AC: 55639 AN: 152068 Hom.: 10287 Cov.: 32 AF XY: 0.366 AC XY: 27230 AN XY: 74338

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.348

Alfa AF: 0.372 Hom.: 18292

Bravo AF: 0.361

Asia WGS AF: 0.382 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.9
DANN	Benign	0.63

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: rs233112; hg19: chr1-85785751;