4-141196270-A-G

Position:

• chr4-141196270-A-G

Variant summary

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

The ENST00000420921.6(RNF150):​c.-6+16524T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,064 control chromosomes in the GnomAD database, including 5,347 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 0.25 (5347 hom., cov: 32)
• Consequence: RNF150 ENST00000420921.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF150	XM_011532148.4	c.-6+16524T>C		intron_variant
RNF150	XM_017008475.2	c.-51+16524T>C		intron_variant
RNF150	XM_047415996.1	c.-51+16524T>C		intron_variant
RNF150	XM_047415998.1	c.-24+16524T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF150	ENST00000420921.6	c.-6+16524T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38361 AN: 151946 Hom.: 5356 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.252 AC: 38359 AN: 152064 Hom.: 5347 Cov.: 32 AF XY: 0.255 AC XY: 18931 AN XY: 74348

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.265

Alfa AF: 0.267 Hom.: 13013

Bravo AF: 0.254

Asia WGS AF: 0.395 AC: 1372 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	0.89
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1550057; hg19: chr4-142117424;