rs6884272

Variant names:

• chr5-179968326-C-A
• rs6884272
• NM_018434.6:c.946-1316G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_018434.6(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 NM_018434.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 0 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 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.946-1316G>T		intron	N/A	NP_060904.2
	RNF130	NM_001410829.1		c.946-1316G>T		intron	N/A	NP_001397758.1
	RNF130	NM_001280801.2		c.946-1316G>T		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.946-1316G>T		intron	N/A	ENSP00000430237.1
	RNF130	ENST00000261947.4	TSL:1	c.946-1316G>T		intron	N/A	ENSP00000261947.4
	RNF130	ENST00000520911.5	TSL:1	n.*465-1316G>T		intron	N/A	ENSP00000430999.1

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

African (AFR) AF: 0.565 AC: 23055 AN: 40818

American (AMR) AF: 0.596 AC: 8869 AN: 14888

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2472 AN: 3432

East Asian (EAS) AF: 0.376 AC: 1888 AN: 5016

South Asian (SAS) AF: 0.613 AC: 2882 AN: 4704

European-Finnish (FIN) AF: 0.575 AC: 5885 AN: 10242

Middle Eastern (MID) AF: 0.785 AC: 223 AN: 284

European-Non Finnish (NFE) AF: 0.618 AC: 40581 AN: 65622

Other (OTH) AF: 0.612 AC: 1258 AN: 2056

Alfa AF: 0.619 Hom.: 42138

Bravo AF: 0.601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.56
PhyloP100		-0.63
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: rs6884272; hg19: chr5-179395326;