chr1-85427706-T-C

Position:

• chr1-85427706-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+37037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.038 in 152,284 control chromosomes in the GnomAD database, including 179 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 0.038 (179 hom., cov: 33)
• Consequence: DDAH1 NM_012137.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

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=-0.47).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDAH1	NM_012137.4	c.303+37037A>G		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+37037A>G		intron_variant		1	NM_012137.4	ENSP00000284031.8
DDAH1	ENST00000426972.8	c.-7+68460A>G		intron_variant		1		ENSP00000411189.4
BCL10-AS1	ENST00000426125.1	n.138-20092T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0381 AC: 5790 AN: 152166 Hom.: 179 Cov.: 33

Gnomad AFR AF: 0.00888

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0540

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0380 AC: 5793 AN: 152284 Hom.: 179 Cov.: 33 AF XY: 0.0382 AC XY: 2845 AN XY: 74452

Gnomad4 AFR AF: 0.00883

Gnomad4 AMR AF: 0.0201

Gnomad4 ASJ AF: 0.0951

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0291

Gnomad4 NFE AF: 0.0540

Gnomad4 OTH AF: 0.0288

Alfa AF: 0.0565 Hom.: 205

Bravo AF: 0.0338

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	12
DANN	Benign	0.87

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: rs17388437; hg19: chr1-85893389;