rs10007052

Variant names:

• chr4-141084419-C-A
• rs10007052
• NM_020724.2:c.484+47906G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-141084419-C-A
• chr4-141084419-C-G
• chr4-141084419-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020724.2(RNF150):​c.484+47906G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,940 control chromosomes in the GnomAD database, including 8,868 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 0.32 (8868 hom., cov: 33)
• Consequence: RNF150 NM_020724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 9 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF150	NM_020724.2	c.484+47906G>T		intron_variant	Intron 1 of 6	ENST00000515673.7	NP_065775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF150	ENST00000515673.7	c.484+47906G>T		intron_variant	Intron 1 of 6	5	NM_020724.2	ENSP00000425840.1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48249 AN: 151822 Hom.: 8858 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.318 AC: 48312 AN: 151940 Hom.: 8868 Cov.: 33 AF XY: 0.323 AC XY: 24012 AN XY: 74254

African (AFR) AF: 0.431 AC: 17832 AN: 41374

American (AMR) AF: 0.312 AC: 4763 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1143 AN: 3470

East Asian (EAS) AF: 0.749 AC: 3871 AN: 5170

South Asian (SAS) AF: 0.471 AC: 2268 AN: 4816

European-Finnish (FIN) AF: 0.224 AC: 2367 AN: 10558

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15207 AN: 67956

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.273 Hom.: 12770

Bravo AF: 0.329

Asia WGS AF: 0.579 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.36
PhyloP100		-0.067
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: rs10007052; hg19: chr4-142005573;