rs3796619

chr4-1101493-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001131034.4(RNF212):c.172-4654T>C variant causes a intron change. The variant allele was found at a frequency of 0.568 in 154,574 control chromosomes in the GnomAD database, including 26,931 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency:
  • Genomes: 𝑓 0.57 (26372 hom., cov: 32)
  • Exomes 𝑓: 0.67 (559 hom.)
• Consequence: RNF212 NM_001131034.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: 4.45

Genes affected

RNF212 (HGNC:27729): (ring finger protein 212) This gene encodes a RING finger protein that may function as a ubiquitin ligase. The encoded protein may be involved in meiotic recombination. This gene is located within a linkage disequilibrium block and polymorphisms in this gene may influence recombination rates. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2010]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF212	NM_001131034.4	c.172-4654T>C		intron_variant		ENST00000433731.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF212	ENST00000433731.7	c.172-4654T>C		intron_variant		1	NM_001131034.4	A2
	ENST00000513176.2	n.66T>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86203 AN: 151974 Hom.: 26385 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.592

GnomAD4 exome AF: 0.674 AC: 1672 AN: 2482 Hom.: 559 Cov.: 0 AF XY: 0.668 AC XY: 844 AN XY: 1264

Gnomad4 AFR exome AF: 0.385

Gnomad4 AMR exome AF: 0.530

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.652

Gnomad4 SAS exome AF: 0.669

Gnomad4 FIN exome AF: 0.693

Gnomad4 NFE exome AF: 0.686

Gnomad4 OTH exome AF: 0.606

GnomAD4 genome AF: 0.567 AC: 86201 AN: 152092 Hom.: 26372 Cov.: 32 AF XY: 0.568 AC XY: 42211 AN XY: 74330

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.588

Alfa AF: 0.664 Hom.: 73164

Bravo AF: 0.545

Asia WGS AF: 0.563 AC: 1957 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Recombination rate quantitative trait locus 1 Other:1

association, no assertion criteria provided

literature only

OMIM

Mar 07, 2008

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.7
Dann	Benign	0.46

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: rs3796619; hg19: chr4-1095281;