chr4-141019559-G-A

Variant names:

• chr4-141019559-G-A
• rs1899424
• NM_020724.2:c.485-51686C>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.485-51686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,136 control chromosomes in the GnomAD database, including 65,998 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 0.93 (65998 hom., cov: 31)
• Consequence: RNF150 NM_020724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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.485-51686C>T		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.485-51686C>T		intron	N/A	ENSP00000425840.1
	RNF150	ENST00000507500.5	TSL:1	c.485-51686C>T		intron	N/A	ENSP00000425568.1
	RNF150	ENST00000306799.7	TSL:1	c.485-51686C>T		intron	N/A	ENSP00000304321.3

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140801 AN: 152018 Hom.: 65963 Cov.: 31

Gnomad AFR AF: 0.764

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.996

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.926 AC: 140892 AN: 152136 Hom.: 65998 Cov.: 31 AF XY: 0.927 AC XY: 68931 AN XY: 74368

African (AFR) AF: 0.764 AC: 31650 AN: 41434

American (AMR) AF: 0.933 AC: 14259 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3433 AN: 3468

East Asian (EAS) AF: 0.967 AC: 5003 AN: 5172

South Asian (SAS) AF: 0.997 AC: 4808 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10607 AN: 10608

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67922 AN: 68022

Other (OTH) AF: 0.949 AC: 2009 AN: 2116

Alfa AF: 0.943 Hom.: 8996

Bravo AF: 0.912

Asia WGS AF: 0.972 AC: 3379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.6
DANN	Benign	0.71
PhyloP100		0.15
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: rs1899424; hg19: chr4-141940713;