chr1-85572793-A-C

Variant names:

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

Variant summary

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

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
• 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124904208	XR_007066200.1	n.3475T>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124904208	XR_007066201.1	n.3133T>G		non_coding_transcript_exon_variant	Exon 2 of 2
DDAH1	NM_001134445.2	c.-123+5191T>G		intron_variant	Intron 1 of 6		NP_001127917.1
DDAH1	XM_005270707.3	c.18+5191T>G		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>G		intron_variant	Intron 1 of 6	1		ENSP00000411189.4
ENSG00000282057	ENST00000467530.5	n.167+5191T>G		intron_variant	Intron 1 of 2	2
ENSG00000282057	ENST00000467666.2	n.275+3039T>G		intron_variant	Intron 2 of 3	3
ENSG00000282057	ENST00000498304.5	n.267+5191T>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135655 AN: 152116 Hom.: 60612 Cov.: 33

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.892 AC: 135742 AN: 152232 Hom.: 60645 Cov.: 33 AF XY: 0.886 AC XY: 65958 AN XY: 74428

African (AFR) AF: 0.903 AC: 37498 AN: 41540

American (AMR) AF: 0.838 AC: 12820 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3273 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4355 AN: 5160

South Asian (SAS) AF: 0.942 AC: 4542 AN: 4822

European-Finnish (FIN) AF: 0.822 AC: 8708 AN: 10598

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61472 AN: 68024

Other (OTH) AF: 0.898 AC: 1900 AN: 2116

Alfa AF: 0.905 Hom.: 76960

Bravo AF: 0.895

Asia WGS AF: 0.895 AC: 3113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.84
PhyloP100		-0.12
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: rs6682848; hg19: chr1-86038476;