chr20-35700304-T-C

Variant names:

• chr20-35700304-T-C
• rs6060566
• NM_080748.3:c.132-494T>C

Variant summary

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

The NM_080748.3(ROMO1):​c.132-494T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,104 control chromosomes in the GnomAD database, including 3,060 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 0.19 (3060 hom., cov: 32)
• Consequence: ROMO1 NM_080748.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 19 publications found

Genes affected

ROMO1 (HGNC:16185): (reactive oxygen species modulator 1) The protein encoded by this gene is a mitochondrial membrane protein that is responsible for increasing the level of reactive oxygen species (ROS) in cells. The protein also has antimicrobial activity against a variety of bacteria by inducing bacterial membrane breakage. [provided by RefSeq, Nov 2014]

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 (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080748.3. 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
	ROMO1	NM_080748.3	MANE Select	c.132-494T>C		intron	N/A	NP_542786.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROMO1	ENST00000374077.8	TSL:1 MANE Select	c.132-494T>C		intron	N/A	ENSP00000363190.3
	ROMO1	ENST00000336695.4	TSL:1	c.132-494T>C		intron	N/A	ENSP00000338293.4
	ROMO1	ENST00000374078.5	TSL:1	c.132-494T>C		intron	N/A	ENSP00000363191.1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28420 AN: 151986 Hom.: 3058 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.187 AC: 28433 AN: 152104 Hom.: 3060 Cov.: 32 AF XY: 0.186 AC XY: 13794 AN XY: 74360

African (AFR) AF: 0.307 AC: 12738 AN: 41454

American (AMR) AF: 0.154 AC: 2353 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 585 AN: 3472

East Asian (EAS) AF: 0.121 AC: 628 AN: 5180

South Asian (SAS) AF: 0.159 AC: 768 AN: 4826

European-Finnish (FIN) AF: 0.140 AC: 1478 AN: 10594

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9299 AN: 67984

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.175 Hom.: 318

Bravo AF: 0.190

Asia WGS AF: 0.199 AC: 689 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	4.7
DANN	Benign	0.43
PhyloP100		-0.15
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: rs6060566; hg19: chr20-34288226;