5-180044201-C-T

Position:

• chr5-180044201-C-T

Variant summary

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

The NM_018434.6(RNF130):​c.248-3554G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,058 control chromosomes in the GnomAD database, including 1,360 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 0.13 (1360 hom., cov: 32)
• Consequence: RNF130 NM_018434.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF130	NM_018434.6	c.248-3554G>A		intron_variant		ENST00000521389.6	NP_060904.2
RNF130	NM_001280801.2	c.248-3554G>A		intron_variant			NP_001267730.1
RNF130	NM_001410829.1	c.248-3554G>A		intron_variant			NP_001397758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF130	ENST00000521389.6	c.248-3554G>A		intron_variant		1	NM_018434.6	ENSP00000430237	P4
RNF130	ENST00000261947.4	c.248-3554G>A		intron_variant		1		ENSP00000261947	A2
RNF130	ENST00000520911.5	c.248-3554G>A		intron_variant, NMD_transcript_variant		1		ENSP00000430999
RNF130	ENST00000522208.6	c.248-3554G>A		intron_variant		5		ENSP00000429509	A1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19122 AN: 151940 Hom.: 1362 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.126 AC: 19132 AN: 152058 Hom.: 1360 Cov.: 32 AF XY: 0.128 AC XY: 9507 AN XY: 74318

Gnomad4 AFR AF: 0.0564

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.123

Alfa AF: 0.154 Hom.: 1923

Bravo AF: 0.120

Asia WGS AF: 0.174 AC: 604 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.039
DANN	Benign	0.62

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: rs13161895; hg19: chr5-179471201;