dbSNP rs7722251: RANBP3L:c.*1004A>C (chr5-36248650-T-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.09

Publications

5 publications found

Variant links:

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]

RANBP3L links:

LOC124900962 (HGNC:):

LOC124900962 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RANBP3L	NM_145000.5 link	c.*1004A>C		3_prime_UTR_variant	Exon 14 of 14	ENST00000296604.8	NP_659437.3	Q86VV4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RANBP3L	ENST00000296604.8 link	c.*1004A>C		3_prime_UTR_variant	Exon 14 of 14	1	NM_145000.5	ENSP00000296604.3		Q86VV4-1

Frequencies

GnomAD3 genomes

AF:

0.875

AC:

132967

AN:

151996

Hom.:

59360

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.875

AC:

133031

AN:

152114

Hom.:

59380

Cov.:

AF XY:

0.875

AC XY:

65042

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.700

AC:

29023

AN:

41432

American (AMR)

AF:

0.861

AC:

13158

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.938

AC:

3258

AN:

3472

East Asian (EAS)

AF:

0.691

AC:

3573

AN:

5172

South Asian (SAS)

AF:

0.934

AC:

4509

AN:

4826

European-Finnish (FIN)

AF:

0.979

AC:

10383

AN:

10610

Middle Eastern (MID)

AF:

0.871

AC:

256

AN:

294

European-Non Finnish (NFE)

AF:

0.972

AC:

66077

AN:

68004

Other (OTH)

AF:

0.893

AC:

1883

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

734

1468

2203

2937

3671

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.931

Hom.:

168809

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 02, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.86

(source)

DANN

Benign

0.61

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs7722251

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over