1-85570890-G-T

Position:

• chr1-85570890-G-T

Variant summary

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

The ENST00000426972.8(DDAH1):​c.-123+7094C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,836 control chromosomes in the GnomAD database, including 8,336 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 0.32 (8336 hom., cov: 32)
• Consequence: DDAH1 ENST00000426972.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

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]

LOC124904208 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904208	XR_007066201.1	n.5036C>A		non_coding_transcript_exon_variant	2/2
DDAH1	NM_001134445.2	c.-123+7094C>A		intron_variant			NP_001127917.1
DDAH1	XM_005270707.3	c.18+7094C>A		intron_variant			XP_005270764.1
LOC124904208	XR_007066200.1	n.5378C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDAH1	ENST00000426972.8	c.-123+7094C>A		intron_variant		1		ENSP00000411189
	ENST00000498304.5	n.267+7094C>A		intron_variant, non_coding_transcript_variant		3
	ENST00000467530.5	n.167+7094C>A		intron_variant, non_coding_transcript_variant		2
	ENST00000467666.2	n.275+4942C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48957 AN: 151718 Hom.: 8326 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.323 AC: 48991 AN: 151836 Hom.: 8336 Cov.: 32 AF XY: 0.325 AC XY: 24083 AN XY: 74210

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.340

Alfa AF: 0.344 Hom.: 12265

Bravo AF: 0.313

Asia WGS AF: 0.514 AC: 1782 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378228; hg19: chr1-86036573;