rs1403956

Variant names:

• chr1-85467955-G-A
• rs1403956
• ENST00000426972.8:c.-7+28211C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426972.8(DDAH1):​c.-7+28211C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,026 control chromosomes in the GnomAD database, including 14,221 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 0.42 (14221 hom., cov: 32)
• Consequence: DDAH1 ENST00000426972.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDAH1	NM_001134445.2	c.-7+28211C>T		intron_variant	Intron 2 of 6		NP_001127917.1
DDAH1	XM_005270707.3	c.19-109108C>T		intron_variant	Intron 1 of 5		XP_005270764.1
DDAH1	XM_011541158.2	c.-87+28211C>T		intron_variant	Intron 1 of 6		XP_011539460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDAH1	ENST00000426972.8	c.-7+28211C>T		intron_variant	Intron 2 of 6	1		ENSP00000411189.4

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63175 AN: 151908 Hom.: 14215 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.416 AC: 63198 AN: 152026 Hom.: 14221 Cov.: 32 AF XY: 0.418 AC XY: 31049 AN XY: 74312

African (AFR) AF: 0.245 AC: 10151 AN: 41460

American (AMR) AF: 0.496 AC: 7573 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1776 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1148 AN: 5170

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4816

European-Finnish (FIN) AF: 0.543 AC: 5726 AN: 10554

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33772 AN: 67972

Other (OTH) AF: 0.441 AC: 930 AN: 2110

Alfa AF: 0.471 Hom.: 77093

Bravo AF: 0.406

Asia WGS AF: 0.297 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.31
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1403956; hg19: chr1-85933638;