rs10519572

Variant names:

• chr4-140951638-T-C
• rs10519572
• NM_020724.2:c.736-2266A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_020724.2(RNF150):​c.736-2266A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0349 in 151,764 control chromosomes in the GnomAD database, including 203 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 0.035 (203 hom., cov: 31)
• Consequence: RNF150 NM_020724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF150	NM_020724.2	c.736-2266A>G		intron_variant	Intron 2 of 6	ENST00000515673.7	NP_065775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF150	ENST00000515673.7	c.736-2266A>G		intron_variant	Intron 2 of 6	5	NM_020724.2	ENSP00000425840.1

Frequencies

GnomAD3 genomes AF: 0.0349 AC: 5285 AN: 151646 Hom.: 203 Cov.: 31

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00250

Gnomad FIN AF: 0.00569

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0280

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

GnomAD4 genome AF: 0.0349 AC: 5298 AN: 151764 Hom.: 203 Cov.: 31 AF XY: 0.0339 AC XY: 2516 AN XY: 74212

African (AFR) AF: 0.0927 AC: 3834 AN: 41338

American (AMR) AF: 0.0200 AC: 305 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3470

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5134

South Asian (SAS) AF: 0.00230 AC: 11 AN: 4790

European-Finnish (FIN) AF: 0.00569 AC: 60 AN: 10536

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0141 AC: 956 AN: 67964

Other (OTH) AF: 0.0277 AC: 58 AN: 2096

Alfa AF: 0.0248 Hom.: 57

Bravo AF: 0.0387

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	16
DANN	Benign	0.38
PhyloP100		0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.39		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.39		Position offset: 1

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

Other links and lift over

dbSNP: rs10519572; hg19: chr4-141872792;