rs354935

Positions:

• chr4-141153962-G-C

Variant summary

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

The ENST00000420921.6(RNF150):​c.-6+58832C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,046 control chromosomes in the GnomAD database, including 11,811 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 0.36 (11811 hom., cov: 32)
• Consequence: RNF150 ENST00000420921.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF150	XM_011532148.4	c.-6+58832C>G		intron_variant			XP_011530450.1
RNF150	XM_017008475.2	c.-50-44005C>G		intron_variant			XP_016863964.1
RNF150	XM_047415996.1	c.-50-44005C>G		intron_variant			XP_047271952.1
RNF150	XM_047415998.1	c.-24+58832C>G		intron_variant			XP_047271954.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF150	ENST00000420921.6	c.-6+58832C>G		intron_variant		2		ENSP00000394581

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54130 AN: 151930 Hom.: 11806 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.356 AC: 54148 AN: 152046 Hom.: 11811 Cov.: 32 AF XY: 0.358 AC XY: 26598 AN XY: 74296

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.373

Alfa AF: 0.409 Hom.: 1773

Bravo AF: 0.341

Asia WGS AF: 0.286 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs354935; hg19: chr4-142075116;