5-36284500-G-T

Variant summary

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

The NM_145000.5(RANBP3L):c.92-13189C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.953 in 152,328 control chromosomes in the GnomAD database, including 69,457 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 0.95 (69457 hom., cov: 33)
• Consequence: RANBP3L NM_145000.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925

Genes affected

RANBP3L (HGNC:26353): (RAN binding protein 3 like) Enables SMAD binding activity. Predicted to be involved in several processes, including mesenchymal cell differentiation involved in bone development; negative regulation of osteoblast differentiation; and positive regulation of myoblast differentiation. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC124900962 (HGNC:):

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 = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RANBP3L	NM_145000.5	c.92-13189C>A		intron_variant		ENST00000296604.8
LOC124900962	XR_007058733.1	n.127+42472G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RANBP3L	ENST00000296604.8	c.92-13189C>A		intron_variant		1	NM_145000.5	A2
RANBP3L	ENST00000502994.5	c.92-13189C>A		intron_variant		2		P4
RANBP3L	ENST00000505865.1	c.92-13189C>A		intron_variant		4
RANBP3L	ENST00000515759.5	c.92-13189C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.953 AC: 145064 AN: 152210 Hom.: 69421 Cov.: 33

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.953 AC: 145154 AN: 152328 Hom.: 69457 Cov.: 33 AF XY: 0.950 AC XY: 70794 AN XY: 74486

Gnomad4 AFR AF: 0.933

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.981

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.966

Alfa AF: 0.974 Hom.: 8275

Bravo AF: 0.943

Asia WGS AF: 0.855 AC: 2972 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	10
Dann	Benign	0.55

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: rs10512637; hg19: chr5-36284602;