rs10519584

Positions:

• chr4-141099748-G-T

Variant summary

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

The NM_020724.2(RNF150):​c.484+32577C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,944 control chromosomes in the GnomAD database, including 1,468 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 (1468 hom., cov: 32)
• Consequence: RNF150 NM_020724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

Genes affected

RNF150 (HGNC:23138): (ring finger protein 150) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in ubiquitin-dependent protein catabolic process. Predicted to be integral component of membrane. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF150	NM_020724.2	c.484+32577C>A		intron_variant		ENST00000515673.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF150	ENST00000515673.7	c.484+32577C>A		intron_variant		5	NM_020724.2	P1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20008 AN: 151826 Hom.: 1472 Cov.: 32

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.132 AC: 20013 AN: 151944 Hom.: 1468 Cov.: 32 AF XY: 0.128 AC XY: 9534 AN XY: 74256

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.137

Alfa AF: 0.144 Hom.: 609

Bravo AF: 0.130

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.52

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: rs10519584; hg19: chr4-142020902;