rs6682848
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000426972.8(DDAH1):c.-123+5191T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,232 control chromosomes in the GnomAD database, including 60,645 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 0.89 ( 60645 hom., cov: 33)
Consequence
DDAH1
ENST00000426972.8 intron
ENST00000426972.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.123
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124904208 | XR_007066201.1 | n.3133T>G | non_coding_transcript_exon_variant | 2/2 | |||
DDAH1 | NM_001134445.2 | c.-123+5191T>G | intron_variant | ||||
DDAH1 | XM_005270707.3 | c.18+5191T>G | intron_variant | ||||
LOC124904208 | XR_007066200.1 | n.3475T>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDAH1 | ENST00000426972.8 | c.-123+5191T>G | intron_variant | 1 | |||||
ENST00000498304.5 | n.267+5191T>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
ENST00000467530.5 | n.167+5191T>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
ENST00000467666.2 | n.275+3039T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.892 AC: 135655AN: 152116Hom.: 60612 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.892 AC: 135742AN: 152232Hom.: 60645 Cov.: 33 AF XY: 0.886 AC XY: 65958AN XY: 74428
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74428
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at