rs2935

Variant names:

• chr1-85451880-G-A
• rs2935
• NM_012137.4:c.303+12863C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-85451880-G-A
• chr1-85451880-G-T

Variant summary

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

The NM_012137.4(DDAH1):​c.303+12863C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,114 control chromosomes in the GnomAD database, including 1,067 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 0.11 (1067 hom., cov: 32)
• Consequence: DDAH1 NM_012137.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 11 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDAH1	NM_012137.4	c.303+12863C>T		intron_variant	Intron 1 of 5	ENST00000284031.13	NP_036269.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDAH1	ENST00000284031.13	c.303+12863C>T		intron_variant	Intron 1 of 5	1	NM_012137.4	ENSP00000284031.8
DDAH1	ENST00000426972.8	c.-7+44286C>T		intron_variant	Intron 2 of 6	1		ENSP00000411189.4

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17386 AN: 151996 Hom.: 1063 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.114 AC: 17405 AN: 152114 Hom.: 1067 Cov.: 32 AF XY: 0.114 AC XY: 8459 AN XY: 74350

African (AFR) AF: 0.100 AC: 4149 AN: 41486

American (AMR) AF: 0.139 AC: 2119 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1233 AN: 5166

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10580

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7790 AN: 67988

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.111 Hom.: 576

Bravo AF: 0.119

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.48
DANN	Benign	0.78
PhyloP100		-0.41
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: rs2935; hg19: chr1-85917563;