1-220806087-C-T

Variant names:

• chr1-220806087-C-T
• rs17008835
• NM_022746.4:c.887+813C>T

Variant summary

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

The NM_022746.4(MTARC1):​c.887+813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,198 control chromosomes in the GnomAD database, including 3,703 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 0.21 (3703 hom., cov: 33)
• Consequence: MTARC1 NM_022746.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

Genes affected

MTARC1 (HGNC:26189): (mitochondrial amidoxime reducing component 1) Enables molybdenum ion binding activity; molybdopterin cofactor binding activity; and oxidoreductase activity, acting on other nitrogenous compounds as donors. Contributes to nitrite reductase (NO-forming) activity. Involved in cellular detoxification of nitrogen compound; nitrate metabolic process; and nitric oxide biosynthetic process. Located in mitochondrion. Part of nitric-oxide synthase complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022746.4. 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
	MTARC1	NM_022746.4	MANE Select	c.887+813C>T		intron	N/A	NP_073583.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTARC1	ENST00000366910.10	TSL:1 MANE Select	c.887+813C>T		intron	N/A	ENSP00000355877.5
	ENSG00000286231	ENST00000651706.1		n.842+813C>T		intron	N/A	ENSP00000499157.1
	MTARC1	ENST00000694919.1		c.1055+813C>T		intron	N/A	ENSP00000511594.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31936 AN: 152080 Hom.: 3696 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.210 AC: 31964 AN: 152198 Hom.: 3703 Cov.: 33 AF XY: 0.216 AC XY: 16047 AN XY: 74412

African (AFR) AF: 0.264 AC: 10949 AN: 41518

American (AMR) AF: 0.256 AC: 3907 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1777 AN: 5176

South Asian (SAS) AF: 0.327 AC: 1580 AN: 4828

European-Finnish (FIN) AF: 0.188 AC: 1990 AN: 10590

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10528 AN: 68012

Other (OTH) AF: 0.197 AC: 417 AN: 2112

Alfa AF: 0.181 Hom.: 3442

Bravo AF: 0.221

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.086
DANN	Benign	0.44
PhyloP100		-1.2
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: rs17008835; hg19: chr1-220979429;