5-179971318-G-C

Position:

• chr5-179971318-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

RNF130 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF130	NM_018434.6	c.849-812C>G		intron_variant		ENST00000521389.6	NP_060904.2
RNF130	NM_001410829.1	c.849-812C>G		intron_variant			NP_001397758.1
RNF130	NM_001280801.2	c.849-812C>G		intron_variant			NP_001267730.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF130	ENST00000521389.6	c.849-812C>G		intron_variant		1	NM_018434.6	ENSP00000430237.1
RNF130	ENST00000520911.5	n.*368-812C>G		intron_variant		1		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

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.574

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs190328; hg19: chr5-179398318; COSMIC: COSV56149260;