5-179971318-G-C

Variant names:

• chr5-179971318-G-C
• rs190328
• NM_018434.6:c.849-812C>G

Variant summary

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

The NM_018434.6(RNF130):​c.849-812C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,062 control chromosomes in the GnomAD database, including 23,563 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 0.54 (23563 hom., cov: 33)
• Consequence: RNF130 NM_018434.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 1 publications found

Genes affected

RNF130 (HGNC:18280): (ring finger protein 130) The protein encoded by this gene contains a RING finger motif and is similar to g1, a Drosophila zinc-finger protein that is expressed in mesoderm and involved in embryonic development. The expression of the mouse counterpart was found to be upregulated in myeloblastic cells following IL3 deprivation, suggesting that this gene may regulate growth factor withdrawal-induced apoptosis of myeloid precursor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018434.6. 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
	RNF130	NM_018434.6	MANE Select	c.849-812C>G		intron	N/A	NP_060904.2
	RNF130	NM_001410829.1		c.849-812C>G		intron	N/A	NP_001397758.1
	RNF130	NM_001280801.2		c.849-812C>G		intron	N/A	NP_001267730.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF130	ENST00000521389.6	TSL:1 MANE Select	c.849-812C>G		intron	N/A	ENSP00000430237.1
	RNF130	ENST00000261947.4	TSL:1	c.849-812C>G		intron	N/A	ENSP00000261947.4
	RNF130	ENST00000520911.5	TSL:1	n.*368-812C>G		intron	N/A	ENSP00000430999.1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81476 AN: 151944 Hom.: 23566 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.536 AC: 81497 AN: 152062 Hom.: 23563 Cov.: 33 AF XY: 0.535 AC XY: 39803 AN XY: 74334

African (AFR) AF: 0.315 AC: 13049 AN: 41476

American (AMR) AF: 0.587 AC: 8960 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2535 AN: 3468

East Asian (EAS) AF: 0.375 AC: 1938 AN: 5170

South Asian (SAS) AF: 0.622 AC: 3002 AN: 4826

European-Finnish (FIN) AF: 0.585 AC: 6177 AN: 10552

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43891 AN: 67978

Other (OTH) AF: 0.574 AC: 1213 AN: 2114

Alfa AF: 0.453 Hom.: 1368

Bravo AF: 0.522

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs190328; hg19: chr5-179398318; COSMIC: COSV56149260;