rs2903696

Positions:

• chr2-109632044-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.8371-209360C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0467 in 152,092 control chromosomes in the GnomAD database, including 628 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 0.047 (628 hom., cov: 32)
• Consequence: RANBP2 XM_047445367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

RANBP2 (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 (EAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RANBP2	XM_047445367.1	c.8371-209360C>T		intron_variant			XP_047301323.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0466 AC: 7080 AN: 151974 Hom.: 618 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0517

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0467 AC: 7102 AN: 152092 Hom.: 628 Cov.: 32 AF XY: 0.0513 AC XY: 3811 AN XY: 74346

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.0517

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.0866

Gnomad4 FIN AF: 0.0202

Gnomad4 NFE AF: 0.0200

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0300 Hom.: 37

Bravo AF: 0.0636

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2903696; hg19: chr2-110389621;