6-13944836-G-T

Variant names:

• chr6-13944836-G-T
• rs280153
• NM_152737.4:c.-367+19813G>T

Variant summary

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

The NM_152737.4(RNF182):​c.-367+19813G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,130 control chromosomes in the GnomAD database, including 52,092 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 0.82 (52092 hom., cov: 31)
• Consequence: RNF182 NM_152737.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 1 publications found

Genes affected

RNF182 (HGNC:28522): (ring finger protein 182) Enables ubiquitin-protein transferase activity. Involved in protein ubiquitination. Located 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152737.4. 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
	RNF182	NM_152737.4	MANE Select	c.-367+19813G>T		intron	N/A	NP_689950.1
	RNF182	NM_001165032.2		c.-449-16644G>T		intron	N/A	NP_001158504.1
	RNF182	NM_001165033.2		c.-212+19470G>T		intron	N/A	NP_001158505.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF182	ENST00000488300.6	TSL:1 MANE Select	c.-367+19813G>T		intron	N/A	ENSP00000420465.1
	RNF182	ENST00000420478.2	TSL:1	c.-212+19813G>T		intron	N/A	ENSP00000419329.1
	RNF182	ENST00000537388.1	TSL:2	c.-212+19470G>T		intron	N/A	ENSP00000441271.1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124848 AN: 152014 Hom.: 52070 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.821 AC: 124926 AN: 152130 Hom.: 52092 Cov.: 31 AF XY: 0.819 AC XY: 60930 AN XY: 74368

African (AFR) AF: 0.674 AC: 27946 AN: 41482

American (AMR) AF: 0.823 AC: 12577 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 3278 AN: 3470

East Asian (EAS) AF: 0.839 AC: 4343 AN: 5176

South Asian (SAS) AF: 0.767 AC: 3695 AN: 4816

European-Finnish (FIN) AF: 0.897 AC: 9501 AN: 10594

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60777 AN: 68002

Other (OTH) AF: 0.843 AC: 1777 AN: 2108

Alfa AF: 0.874 Hom.: 25408

Bravo AF: 0.810

Asia WGS AF: 0.788 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.37
PhyloP100		-0.20
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: rs280153; hg19: chr6-13945067;