rs6884272

Positions:

• chr5-179968326-C-A
• chr5-179968326-C-T

Variant summary

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

The ENST00000521389.6(RNF130):​c.946-1316G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 147,924 control chromosomes in the GnomAD database, including 25,578 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 0.59 (25578 hom., cov: 30)
• Consequence: RNF130 ENST00000521389.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF130	NM_018434.6	c.946-1316G>T		intron_variant		ENST00000521389.6	NP_060904.2
RNF130	NM_001280801.2	c.946-1316G>T		intron_variant			NP_001267730.1
RNF130	NM_001410829.1	c.946-1316G>T		intron_variant			NP_001397758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF130	ENST00000521389.6	c.946-1316G>T		intron_variant		1	NM_018434.6	ENSP00000430237	P4

Frequencies

GnomAD3 genomes AF: 0.592 AC: 87485 AN: 147804 Hom.: 25549 Cov.: 30

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.773

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.592 AC: 87570 AN: 147924 Hom.: 25578 Cov.: 30 AF XY: 0.591 AC XY: 42713 AN XY: 72296

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.612

Alfa AF: 0.563 Hom.: 3031

Bravo AF: 0.601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.56

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: rs6884272; hg19: chr5-179395326;