1-85465439-T-TGCAC

Position:

• chr1-85465439-T-TGCAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001134445.2(DDAH1):​c.-7+30723_-7+30726dupGTGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,136 control chromosomes in the GnomAD database, including 1,063 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (1063 hom., cov: 31)
• Consequence: DDAH1 NM_001134445.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.34

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 -10 ACMG points.

• BP6: Variant 1-85465439-T-TGCAC is Benign according to our data. Variant chr1-85465439-T-TGCAC is described in ClinVar as [Benign]. Clinvar id is 1289550.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDAH1	NM_001134445.2	c.-7+30723_-7+30726dupGTGC		intron_variant			NP_001127917.1
DDAH1	XM_005270707.3	c.19-106596_19-106593dupGTGC		intron_variant			XP_005270764.1
DDAH1	XM_011541158.2	c.-87+30723_-87+30726dupGTGC		intron_variant			XP_011539460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDAH1	ENST00000426972.8	c.-7+30723_-7+30726dupGTGC		intron_variant		1		ENSP00000411189.4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16091 AN: 152018 Hom.: 1064 Cov.: 31

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0854

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.106 AC: 16089 AN: 152136 Hom.: 1063 Cov.: 31 AF XY: 0.109 AC XY: 8088 AN XY: 74378

Gnomad4 AFR AF: 0.0384

Gnomad4 AMR AF: 0.0854

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0856

Alfa AF: 0.122 Hom.: 144

Bravo AF: 0.0964

Asia WGS AF: 0.184 AC: 637 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 19, 2019

This variant is associated with the following publications: (PMID: 20167924, 31733101) -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs150767365; hg19: chr1-85931122;