1-85572793-A-G

Variant names:

• chr1-85572793-A-G
• rs6682848
• ENST00000426972.8:c.-123+5191T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000426972.8(DDAH1):​c.-123+5191T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: DDAH1 ENST00000426972.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 3 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]

LOC124904208 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904208	XR_007066200.1	n.3475T>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124904208	XR_007066201.1	n.3133T>C		non_coding_transcript_exon_variant	Exon 2 of 2
DDAH1	NM_001134445.2	c.-123+5191T>C		intron_variant	Intron 1 of 6		NP_001127917.1
DDAH1	XM_005270707.3	c.18+5191T>C		intron_variant	Intron 1 of 5		XP_005270764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDAH1	ENST00000426972.8	c.-123+5191T>C		intron_variant	Intron 1 of 6	1		ENSP00000411189.4
ENSG00000282057	ENST00000467530.5	n.167+5191T>C		intron_variant	Intron 1 of 2	2
ENSG00000282057	ENST00000467666.2	n.275+3039T>C		intron_variant	Intron 2 of 3	3
ENSG00000282057	ENST00000498304.5	n.267+5191T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.87
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs6682848; hg19: chr1-86038476;