1-220816358-G-T

Variant names:

• chr1-220816358-G-T
• rs7530493
• NM_022746.4:c.*2940G>T

Variant summary

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

The NM_022746.4(MTARC1):​c.*2940G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,166 control chromosomes in the GnomAD database, including 3,415 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 0.20 (3415 hom., cov: 32)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: MTARC1 NM_022746.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

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

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 = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTARC1	NM_022746.4	c.*2940G>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000366910.10	NP_073583.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTARC1	ENST00000366910.10	c.*2940G>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_022746.4	ENSP00000355877.5
ENSG00000286231	ENST00000651706.1	n.842+11084G>T		intron_variant	Intron 6 of 8			ENSP00000499157.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30964 AN: 152024 Hom.: 3402 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.205

GnomAD4 exome AF: 0.0833 AC: 2 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.0909 AC XY: 2 AN XY: 22

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.204 AC: 31010 AN: 152142 Hom.: 3415 Cov.: 32 AF XY: 0.208 AC XY: 15494 AN XY: 74368

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.202

Alfa AF: 0.162 Hom.: 4388

Bravo AF: 0.214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.86

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: rs7530493; hg19: chr1-220989700;