rs2284798

Variant summary

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

The NM_012137.4(DDAH1):​c.597+1520T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 152,284 control chromosomes in the GnomAD database, including 297 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 0.053 ( 297 hom., cov: 32)

Consequence

DDAH1
NM_012137.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.208
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]
BCL10-AS1 (HGNC:55868): (BCL10 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DDAH1NM_012137.4 linkuse as main transcriptc.597+1520T>C intron_variant ENST00000284031.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DDAH1ENST00000284031.13 linkuse as main transcriptc.597+1520T>C intron_variant 1 NM_012137.4 P1O94760-1
BCL10-AS1ENST00000426125.1 linkuse as main transcriptn.68-27871A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0535
AC:
8144
AN:
152166
Hom.:
297
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0500
Gnomad AMI
AF:
0.0592
Gnomad AMR
AF:
0.0314
Gnomad ASJ
AF:
0.0435
Gnomad EAS
AF:
0.160
Gnomad SAS
AF:
0.184
Gnomad FIN
AF:
0.0484
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0447
Gnomad OTH
AF:
0.0478
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0535
AC:
8143
AN:
152284
Hom.:
297
Cov.:
32
AF XY:
0.0564
AC XY:
4200
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.0499
Gnomad4 AMR
AF:
0.0314
Gnomad4 ASJ
AF:
0.0435
Gnomad4 EAS
AF:
0.160
Gnomad4 SAS
AF:
0.184
Gnomad4 FIN
AF:
0.0484
Gnomad4 NFE
AF:
0.0447
Gnomad4 OTH
AF:
0.0477
Alfa
AF:
0.0438
Hom.:
20
Bravo
AF:
0.0500
Asia WGS
AF:
0.138
AC:
479
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
11
DANN
Benign
0.85

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: rs2284798; hg19: chr1-85814578; API