1-85438655-C-T

Position:

• chr1-85438655-C-T

Variant summary

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

The NM_012137.4(DDAH1):​c.303+26088G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,158 control chromosomes in the GnomAD database, including 50,952 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 0.82 (50952 hom., cov: 32)
• Consequence: DDAH1 NM_012137.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDAH1	NM_012137.4	c.303+26088G>A		intron_variant		ENST00000284031.13	NP_036269.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDAH1	ENST00000284031.13	c.303+26088G>A		intron_variant		1	NM_012137.4	ENSP00000284031.8
DDAH1	ENST00000426972.8	c.-7+57511G>A		intron_variant		1		ENSP00000411189.4
BCL10-AS1	ENST00000426125.1	n.138-9143C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124197 AN: 152038 Hom.: 50912 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.817 AC: 124295 AN: 152158 Hom.: 50952 Cov.: 32 AF XY: 0.816 AC XY: 60680 AN XY: 74372

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.857

Alfa AF: 0.840 Hom.: 79902

Bravo AF: 0.822

Asia WGS AF: 0.803 AC: 2795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.73

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: rs539714; hg19: chr1-85904338;