rs10519572

chr4-140951638-T-C

Variant summary

Our verdict is Benign. Variant got -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

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 -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/exons	MANE	UniProt
RNF150	NM_020724.2	c.736-2266A>G		intron_variant		ENST00000515673.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF150	ENST00000515673.7	c.736-2266A>G		intron_variant		5	NM_020724.2	P1

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

Gnomad4 AFR AF: 0.0927

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.00230

Gnomad4 FIN AF: 0.00569

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0277

Alfa AF: 0.0245 Hom.: 32

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519572; hg19: chr4-141872792;