rs11692886

Positions:

• chr2-109516602-C-T

Variant summary

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

The XM_047445367.1(RANBP2):​c.8371-324802C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,168 control chromosomes in the GnomAD database, including 4,141 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 0.22 (4141 hom., cov: 33)
• Consequence: RANBP2 XM_047445367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

Genes affected

RANBP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RANBP2	XM_047445367.1	c.8371-324802C>T		intron_variant			XP_047301323.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32861 AN: 152050 Hom.: 4143 Cov.: 33

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.216 AC: 32856 AN: 152168 Hom.: 4141 Cov.: 33 AF XY: 0.214 AC XY: 15884 AN XY: 74394

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.229

Alfa AF: 0.246 Hom.: 799

Bravo AF: 0.209

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11692886; hg19: chr2-110274179;