rs41411047

Variant names:

• chr3-149875124-G-A
• rs41411047
• NM_183381.3:c.321+2970G>A

Variant summary

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

The NM_183381.3(RNF13):​c.321+2970G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,018 control chromosomes in the GnomAD database, including 490 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 0.077 (490 hom., cov: 32)
• Consequence: RNF13 NM_183381.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 6 publications found

Genes affected

RNF13 (HGNC:10057): (ring finger protein 13) The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. The specific function of this gene has not yet been determined. Alternatively spliced transcript variants that encode the same protein have been reported. A pseudogene, which is also located on chromosome 3, has been defined for this gene. [provided by RefSeq, Jul 2008]

ANKUB1 (HGNC:29642): (ankyrin repeat and ubiquitin domain containing 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNF13	NM_183381.3	c.321+2970G>A		intron_variant	Intron 4 of 9	ENST00000392894.8	NP_899237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF13	ENST00000392894.8	c.321+2970G>A		intron_variant	Intron 4 of 9	1	NM_183381.3	ENSP00000376628.3

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11712 AN: 151898 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.0890

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0485

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0566

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0663

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

GnomAD4 genome AF: 0.0772 AC: 11736 AN: 152018 Hom.: 490 Cov.: 32 AF XY: 0.0773 AC XY: 5743 AN XY: 74310

African (AFR) AF: 0.0891 AC: 3698 AN: 41500

American (AMR) AF: 0.0589 AC: 899 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0485 AC: 168 AN: 3464

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0581 AC: 280 AN: 4816

European-Finnish (FIN) AF: 0.119 AC: 1258 AN: 10556

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0745 AC: 5063 AN: 67932

Other (OTH) AF: 0.0646 AC: 136 AN: 2106

Alfa AF: 0.0738 Hom.: 133

Bravo AF: 0.0736

Asia WGS AF: 0.0250 AC: 88 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.55
PhyloP100		0.80
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: rs41411047; hg19: chr3-149592911;