rs1010342

Positions:

• chr4-1075031-G-A

Variant summary

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

The NM_001131034.4(RNF212):​c.511-1369C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,184 control chromosomes in the GnomAD database, including 48,468 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 0.79 (48468 hom., cov: 33)
• Consequence: RNF212 NM_001131034.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF212	NM_001131034.4	c.511-1369C>T		intron_variant		ENST00000433731.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF212	ENST00000433731.7	c.511-1369C>T		intron_variant		1	NM_001131034.4	A2

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120823 AN: 152066 Hom.: 48451 Cov.: 33

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.794 AC: 120887 AN: 152184 Hom.: 48468 Cov.: 33 AF XY: 0.791 AC XY: 58824 AN XY: 74390

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.782

Alfa AF: 0.776 Hom.: 45689

Bravo AF: 0.787

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.66

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: rs1010342; hg19: chr4-1068819;