5-179923387-T-C

Variant names:

• chr5-179923387-T-C
• rs248232
• NM_001410829.1:c.1151-2961A>G

Variant summary

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

The NM_001410829.1(RNF130):​c.1151-2961A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,132 control chromosomes in the GnomAD database, including 27,695 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 0.57 (27695 hom., cov: 32)
• Consequence: RNF130 NM_001410829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 3 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=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF130	NM_001410829.1	c.1151-2961A>G		intron_variant	Intron 7 of 7		NP_001397758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF130	ENST00000522208.6	c.1151-2961A>G		intron_variant	Intron 7 of 7	5		ENSP00000429509.1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86810 AN: 152014 Hom.: 27644 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.571 AC: 86915 AN: 152132 Hom.: 27695 Cov.: 32 AF XY: 0.576 AC XY: 42841 AN XY: 74364

African (AFR) AF: 0.843 AC: 35015 AN: 41514

American (AMR) AF: 0.645 AC: 9860 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1835 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3898 AN: 5176

South Asian (SAS) AF: 0.597 AC: 2876 AN: 4816

European-Finnish (FIN) AF: 0.450 AC: 4760 AN: 10568

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26967 AN: 67984

Other (OTH) AF: 0.561 AC: 1183 AN: 2108

Alfa AF: 0.463 Hom.: 9958

Bravo AF: 0.597

Asia WGS AF: 0.682 AC: 2372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	7.7
DANN	Benign	0.90
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs248232; hg19: chr5-179350387;