rs6060567

chr20-35700328-G-C

Variant summary

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

The NM_080748.3(ROMO1):c.132-470G>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 152,036 control chromosomes in the GnomAD database, including 3,061 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 (3061 hom., cov: 32)
• Consequence: ROMO1 NM_080748.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.661

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ROMO1	NM_080748.3	c.132-470G>C		intron_variant		ENST00000374077.8
ROMO1	XM_017027678.2	c.132-470G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ROMO1	ENST00000374077.8	c.132-470G>C		intron_variant		1	NM_080748.3	P1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28419 AN: 151918 Hom.: 3059 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.159

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: 28432 AN: 152036 Hom.: 3061 Cov.: 32 AF XY: 0.186 AC XY: 13792 AN XY: 74306

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.184

Alfa AF: 0.168 Hom.: 296

Bravo AF: 0.190

Asia WGS AF: 0.199 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.9
Dann	Benign	0.32

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: rs6060567; hg19: chr20-34288250;