4-1078432-C-T

Position:

• chr4-1078432-C-T

Variant summary

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

The NM_001131034.4(RNF212):​c.510+1211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,960 control chromosomes in the GnomAD database, including 26,291 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 0.57 (26291 hom., cov: 31)
• Consequence: RNF212 NM_001131034.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF212	NM_001131034.4	c.510+1211G>A		intron_variant		ENST00000433731.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF212	ENST00000433731.7	c.510+1211G>A		intron_variant		1	NM_001131034.4	A2

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85919 AN: 151842 Hom.: 26306 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.565 AC: 85917 AN: 151960 Hom.: 26291 Cov.: 31 AF XY: 0.567 AC XY: 42082 AN XY: 74268

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.588

Alfa AF: 0.590 Hom.: 5372

Bravo AF: 0.544

Asia WGS AF: 0.562 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.59

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: rs1466215; hg19: chr4-1072220;