rs13161895

Variant names:

• chr5-180044201-C-T
• rs13161895
• NM_018434.6:c.248-3554G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 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=-0.98).
• 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 rank	MANE	Protein	UniProt
RNF130	NM_018434.6	c.248-3554G>A		intron_variant	Intron 1 of 8	ENST00000521389.6	NP_060904.2
RNF130	NM_001410829.1	c.248-3554G>A		intron_variant	Intron 1 of 7		NP_001397758.1
RNF130	NM_001280801.2	c.248-3554G>A		intron_variant	Intron 1 of 7		NP_001267730.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF130	ENST00000521389.6	c.248-3554G>A		intron_variant	Intron 1 of 8	1	NM_018434.6	ENSP00000430237.1
RNF130	ENST00000261947.4	c.248-3554G>A		intron_variant	Intron 1 of 7	1		ENSP00000261947.4
RNF130	ENST00000520911.5	n.248-3554G>A		intron_variant	Intron 1 of 8	1		ENSP00000430999.1
RNF130	ENST00000522208.6	c.248-3554G>A		intron_variant	Intron 1 of 7	5		ENSP00000429509.1

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

African (AFR) AF: 0.0564 AC: 2340 AN: 41508

American (AMR) AF: 0.124 AC: 1901 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1276 AN: 5176

South Asian (SAS) AF: 0.183 AC: 883 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1556 AN: 10534

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10121 AN: 67960

Other (OTH) AF: 0.123 AC: 259 AN: 2110

Alfa AF: 0.144 Hom.: 3029

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
PhyloP100		-2.2
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: rs13161895; hg19: chr5-179471201;