6-13944836-G-T

Position:

• chr6-13944836-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF182	NM_152737.4	c.-367+19813G>T		intron_variant		ENST00000488300.6	NP_689950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF182	ENST00000488300.6	c.-367+19813G>T		intron_variant		1	NM_152737.4	ENSP00000420465.1

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

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.945

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.843

Alfa AF: 0.875 Hom.: 22182

Bravo AF: 0.810

Asia WGS AF: 0.788 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs280153; hg19: chr6-13945067;