chr4-141103168-T-G

Variant names:

• chr4-141103168-T-G
• rs4629541
• NM_020724.2:c.484+29157A>C

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+29157A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,112 control chromosomes in the GnomAD database, including 45,946 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 0.77 (45946 hom., cov: 31)
• Consequence: RNF150 NM_020724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020724.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF150	NM_020724.2	MANE Select	c.484+29157A>C		intron	N/A	NP_065775.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF150	ENST00000515673.7	TSL:5 MANE Select	c.484+29157A>C		intron	N/A	ENSP00000425840.1
	RNF150	ENST00000507500.5	TSL:1	c.484+29157A>C		intron	N/A	ENSP00000425568.1
	RNF150	ENST00000306799.7	TSL:1	c.484+29157A>C		intron	N/A	ENSP00000304321.3

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116813 AN: 151994 Hom.: 45934 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.768 AC: 116870 AN: 152112 Hom.: 45946 Cov.: 31 AF XY: 0.774 AC XY: 57508 AN XY: 74336

African (AFR) AF: 0.582 AC: 24144 AN: 41454

American (AMR) AF: 0.842 AC: 12868 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3015 AN: 3472

East Asian (EAS) AF: 0.883 AC: 4570 AN: 5174

South Asian (SAS) AF: 0.845 AC: 4073 AN: 4820

European-Finnish (FIN) AF: 0.885 AC: 9371 AN: 10592

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56171 AN: 68008

Other (OTH) AF: 0.794 AC: 1677 AN: 2112

Alfa AF: 0.807 Hom.: 172046

Bravo AF: 0.757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.14
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: rs4629541; hg19: chr4-142024322;