chr5-179950085-T-C

Variant names:

• chr5-179950085-T-C
• rs248328
• NM_001410829.1:c.1150+16721A>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.1150+16721A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,982 control chromosomes in the GnomAD database, including 23,677 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 0.54 (23677 hom., cov: 31)
• Consequence: RNF130 NM_001410829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 2 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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF130	NM_001410829.1	c.1150+16721A>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.1150+16721A>G		intron_variant	Intron 7 of 7	5		ENSP00000429509.1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81639 AN: 151864 Hom.: 23681 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.537 AC: 81657 AN: 151982 Hom.: 23677 Cov.: 31 AF XY: 0.537 AC XY: 39870 AN XY: 74284

African (AFR) AF: 0.314 AC: 13028 AN: 41438

American (AMR) AF: 0.588 AC: 8971 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1956 AN: 5168

South Asian (SAS) AF: 0.621 AC: 2991 AN: 4816

European-Finnish (FIN) AF: 0.588 AC: 6188 AN: 10530

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44029 AN: 67980

Other (OTH) AF: 0.574 AC: 1210 AN: 2108

Alfa AF: 0.566 Hom.: 3951

Bravo AF: 0.523

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.91
PhyloP100		0.28
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: rs248328; hg19: chr5-179377085; COSMIC: COSV73015994; COSMIC: COSV73015994;