rs7666238

Variant names:

• chr4-141174609-A-G
• rs7666238
• ENST00000420921.6:c.-6+38185T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-141174609-A-G
• chr4-141174609-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420921.6(RNF150):​c.-6+38185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,074 control chromosomes in the GnomAD database, including 3,371 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 0.20 (3371 hom., cov: 31)
• Consequence: RNF150 ENST00000420921.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• 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]

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 (SAS) allele frequency at 95% confidence interval = 0.327 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+38185T>C		intron	N/A	ENSP00000394581.2	Q9ULK6-4

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30331 AN: 151956 Hom.: 3374 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.200 AC: 30347 AN: 152074 Hom.: 3371 Cov.: 31 AF XY: 0.201 AC XY: 14925 AN XY: 74340

African (AFR) AF: 0.107 AC: 4446 AN: 41500

American (AMR) AF: 0.223 AC: 3398 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1126 AN: 3470

East Asian (EAS) AF: 0.169 AC: 872 AN: 5172

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4814

European-Finnish (FIN) AF: 0.220 AC: 2331 AN: 10578

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15744 AN: 67954

Other (OTH) AF: 0.226 AC: 477 AN: 2112

Alfa AF: 0.221 Hom.: 11958

Bravo AF: 0.194

Asia WGS AF: 0.258 AC: 896 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	2.4
DANN	Benign	0.71
PhyloP100		0.081
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: rs7666238;

hg19: chr4-142095763;