1-220756014-T-C

Position:

• chr1-220756014-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017898.5(MTARC2):​c.446+894T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,226 control chromosomes in the GnomAD database, including 1,820 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 0.13 (1820 hom., cov: 33)
• Consequence: MTARC2 NM_017898.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

MTARC2 (HGNC:26064): (mitochondrial amidoxime reducing component 2) The protein encoded by this gene is an enzyme found in the outer mitochondrial membrane that reduces N-hydroxylated substrates. The encoded protein uses molybdenum as a cofactor and cytochrome b5 type B and NADH cytochrome b5 reductase as accessory proteins. One type of substrate used is N-hydroxylated nucleotide base analogues, which can be toxic to a cell. Other substrates include N(omega)-hydroxy-L-arginine (NOHA) and amidoxime prodrugs, which are activated by the encoded enzyme. Multiple transcript variants encoding the different isoforms have been found for this gene. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTARC2	NM_017898.5	c.446+894T>C		intron_variant		ENST00000366913.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTARC2	ENST00000366913.8	c.446+894T>C		intron_variant		1	NM_017898.5	P1
MTARC2	ENST00000359316.6	c.446+894T>C		intron_variant		1
MTARC2	ENST00000425560.1	c.149+894T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20273 AN: 152108 Hom.: 1812 Cov.: 33

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.133 AC: 20287 AN: 152226 Hom.: 1820 Cov.: 33 AF XY: 0.138 AC XY: 10289 AN XY: 74446

Gnomad4 AFR AF: 0.0484

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.146

Alfa AF: 0.147 Hom.: 2193

Bravo AF: 0.140

Asia WGS AF: 0.206 AC: 719 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	1.9
DANN	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs1494373; hg19: chr1-220929356;