rs13373844

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012137.4(DDAH1):​c.303+10667T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,740 control chromosomes in the GnomAD database, including 5,086 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 0.25 ( 5086 hom., cov: 31)

Consequence

DDAH1
NM_012137.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.352
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DDAH1NM_012137.4 linkuse as main transcriptc.303+10667T>G intron_variant ENST00000284031.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DDAH1ENST00000284031.13 linkuse as main transcriptc.303+10667T>G intron_variant 1 NM_012137.4 P1O94760-1
DDAH1ENST00000426972.8 linkuse as main transcriptc.-7+42090T>G intron_variant 1 O94760-2

Frequencies

GnomAD3 genomes
AF:
0.253
AC:
38375
AN:
151626
Hom.:
5078
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.198
Gnomad AMI
AF:
0.195
Gnomad AMR
AF:
0.304
Gnomad ASJ
AF:
0.252
Gnomad EAS
AF:
0.0811
Gnomad SAS
AF:
0.228
Gnomad FIN
AF:
0.283
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.285
Gnomad OTH
AF:
0.268
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.253
AC:
38396
AN:
151740
Hom.:
5086
Cov.:
31
AF XY:
0.253
AC XY:
18767
AN XY:
74118
show subpopulations
Gnomad4 AFR
AF:
0.198
Gnomad4 AMR
AF:
0.304
Gnomad4 ASJ
AF:
0.252
Gnomad4 EAS
AF:
0.0815
Gnomad4 SAS
AF:
0.228
Gnomad4 FIN
AF:
0.283
Gnomad4 NFE
AF:
0.285
Gnomad4 OTH
AF:
0.269
Alfa
AF:
0.249
Hom.:
1768
Bravo
AF:
0.251
Asia WGS
AF:
0.193
AC:
671
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
4.0
DANN
Benign
0.58

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13373844; hg19: chr1-85919759; API