5-36248650-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_145000.5(RANBP3L):c.*1004A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,114 control chromosomes in the GnomAD database, including 59,380 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.87 (59380 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: RANBP3L NM_145000.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.09

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 5-36248650-T-G is Benign according to our data. Variant chr5-36248650-T-G is described in ClinVar as [Benign]. Clinvar id is 2785882.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RANBP3L	NM_145000.5	c.*1004A>C		3_prime_UTR_variant	14/14	ENST00000296604.8
LOC124900962	XR_007058733.1	n.127+6622T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RANBP3L	ENST00000296604.8	c.*1004A>C		3_prime_UTR_variant	14/14	1	NM_145000.5	A2

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132967 AN: 151996 Hom.: 59360 Cov.: 31

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.893

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.875 AC: 133031 AN: 152114 Hom.: 59380 Cov.: 31 AF XY: 0.875 AC XY: 65042 AN XY: 74358

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.979

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.893

Alfa AF: 0.952 Hom.: 100077

Bravo AF: 0.855

Asia WGS AF: 0.825 AC: 2868 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 17, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.86
Dann	Benign	0.61

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: rs7722251; hg19: chr5-36248752;