chr5-179923387-T-C

Position:

• chr5-179923387-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	Protein	UniProt
RNF130	NM_001410829.1	c.1151-2961A>G		intron_variant			NP_001397758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF130	ENST00000522208.6	c.1151-2961A>G		intron_variant		5		ENSP00000429509	A1

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

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.561

Alfa AF: 0.466 Hom.: 9172

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs248232; hg19: chr5-179350387;