chr4-141153962-G-C

Variant names:

• chr4-141153962-G-C
• rs354935
• ENST00000420921.6:c.-6+58832C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ENSG00000307939 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420921.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF150	ENST00000420921.6	TSL:2	c.-6+58832C>G		intron	N/A	ENSP00000394581.2	Q9ULK6-4
	ENSG00000307939	ENST00000829932.1		n.143+5831C>G		intron	N/A

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

African (AFR) AF: 0.104 AC: 4328 AN: 41508

American (AMR) AF: 0.461 AC: 7034 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1573 AN: 3468

East Asian (EAS) AF: 0.170 AC: 879 AN: 5182

South Asian (SAS) AF: 0.355 AC: 1707 AN: 4814

European-Finnish (FIN) AF: 0.510 AC: 5376 AN: 10546

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31988 AN: 67950

Other (OTH) AF: 0.373 AC: 788 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.61
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs354935;

hg19: chr4-142075116;