1-85321435-G-C

Variant names:

• chr1-85321435-G-C
• rs3087894
• NM_012137.4:c.*17C>G

Variant summary

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

The ENST00000284031.13(DDAH1):​c.*17C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,556,668 control chromosomes in the GnomAD database, including 102,191 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 0.29 (7250 hom., cov: 31)
  • Exomes 𝑓: 0.37 (94941 hom.)
• Consequence: DDAH1 ENST00000284031.13 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 15 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]

BCL10-AS1 (HGNC:55868): (BCL10 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000284031.13. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDAH1	NM_012137.4	MANE Select	c.*17C>G		3_prime_UTR	Exon 6 of 6	NP_036269.1
	DDAH1	NM_001330655.2		c.*17C>G		3_prime_UTR	Exon 6 of 6	NP_001317584.1
	DDAH1	NM_001134445.2		c.*17C>G		3_prime_UTR	Exon 7 of 7	NP_001127917.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDAH1	ENST00000284031.13	TSL:1 MANE Select	c.*17C>G		3_prime_UTR	Exon 6 of 6	ENSP00000284031.8
	DDAH1	ENST00000426972.8	TSL:1	c.*17C>G		3_prime_UTR	Exon 7 of 7	ENSP00000411189.4
	BCL10-AS1	ENST00000426125.1	TSL:3	n.67+43697G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43899 AN: 151848 Hom.: 7251 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.278

GnomAD2 exomes AF: 0.343 AC: 85847 AN: 249954 AF XY: 0.352

Gnomad AFR exome AF: 0.114

Gnomad AMR exome AF: 0.347

Gnomad ASJ exome AF: 0.331

Gnomad EAS exome AF: 0.300

Gnomad FIN exome AF: 0.395

Gnomad NFE exome AF: 0.357

Gnomad OTH exome AF: 0.341

GnomAD4 exome AF: 0.366 AC: 513649 AN: 1404704 Hom.: 94941 Cov.: 24 AF XY: 0.366 AC XY: 257044 AN XY: 701904

African (AFR) AF: 0.112 AC: 3582 AN: 31886

American (AMR) AF: 0.342 AC: 15226 AN: 44460

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 8321 AN: 25638

East Asian (EAS) AF: 0.258 AC: 10113 AN: 39240

South Asian (SAS) AF: 0.408 AC: 34671 AN: 84882

European-Finnish (FIN) AF: 0.395 AC: 20969 AN: 53032

Middle Eastern (MID) AF: 0.293 AC: 1621 AN: 5530

European-Non Finnish (NFE) AF: 0.376 AC: 399200 AN: 1061768

Other (OTH) AF: 0.342 AC: 19946 AN: 58268

GnomAD4 genome AF: 0.289 AC: 43893 AN: 151964 Hom.: 7250 Cov.: 31 AF XY: 0.292 AC XY: 21697 AN XY: 74268

African (AFR) AF: 0.121 AC: 5003 AN: 41482

American (AMR) AF: 0.317 AC: 4842 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1160 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1473 AN: 5164

South Asian (SAS) AF: 0.403 AC: 1937 AN: 4812

European-Finnish (FIN) AF: 0.380 AC: 4016 AN: 10560

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24466 AN: 67904

Other (OTH) AF: 0.277 AC: 583 AN: 2106

Alfa AF: 0.216 Hom.: 649

Bravo AF: 0.273

Asia WGS AF: 0.293 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.15
DANN	Benign	0.54
PhyloP100		-0.87
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3087894; hg19: chr1-85787118; COSMIC: COSV52303953; COSMIC: COSV52303953;