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. Variant got -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

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF150	XM_047415996.1	c.-51+38185T>C		intron_variant	Intron 1 of 8		XP_047271952.1
RNF150	XM_011532148.4	c.-6+38185T>C		intron_variant	Intron 1 of 7		XP_011530450.1
RNF150	XM_017008475.2	c.-51+38185T>C		intron_variant	Intron 1 of 7		XP_016863964.1
RNF150	XM_047415998.1	c.-24+38185T>C		intron_variant	Intron 1 of 6		XP_047271954.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF150	ENST00000420921.6	c.-6+38185T>C		intron_variant	Intron 1 of 7	2		ENSP00000394581.2

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

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.226

Alfa AF: 0.227 Hom.: 7156

Bravo AF: 0.194

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7666238; hg19: chr4-142095763;