rs4676049

chr2-109018801-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.8370+245755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,208 control chromosomes in the GnomAD database, including 1,894 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 0.13 (1894 hom., cov: 33)
• Consequence: RANBP2 XM_047445367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.48

Genes affected

RANBP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RANBP2	XM_047445367.1	c.8370+245755C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19871 AN: 152090 Hom.: 1892 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.0410

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.131 AC: 19902 AN: 152208 Hom.: 1894 Cov.: 33 AF XY: 0.126 AC XY: 9405 AN XY: 74438

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0758

Gnomad4 FIN AF: 0.0410

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0856 Hom.: 1497

Bravo AF: 0.143

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.040
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4676049; hg19: chr2-109635257;