chr3-77040961-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001395656.1(ROBO2):​c.61+115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 1,392,942 control chromosomes in the GnomAD database, including 5,171 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.058 ( 330 hom., cov: 32)
Exomes 𝑓: 0.083 ( 4841 hom. )

Consequence

ROBO2
NM_001395656.1 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0350
Variant links:
Genes affected
ROBO2 (HGNC:10250): (roundabout guidance receptor 2) The protein encoded by this gene belongs to the ROBO family, part of the immunoglobulin superfamily of proteins that are highly conserved from fly to human. The encoded protein is a transmembrane receptor for the slit homolog 2 protein and functions in axon guidance and cell migration. Mutations in this gene are associated with vesicoureteral reflux, characterized by the backward flow of urine from the bladder into the ureters or the kidney. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 3-77040961-C-T is Benign according to our data. Variant chr3-77040961-C-T is described in ClinVar as [Benign]. Clinvar id is 1247361.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0896 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ROBO2NM_001395656.1 linkuse as main transcriptc.61+115C>T intron_variant ENST00000696593.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ROBO2ENST00000696593.1 linkuse as main transcriptc.61+115C>T intron_variant NM_001395656.1 A2

Frequencies

GnomAD3 genomes
AF:
0.0577
AC:
8602
AN:
149006
Hom.:
331
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0172
Gnomad AMI
AF:
0.0299
Gnomad AMR
AF:
0.0386
Gnomad ASJ
AF:
0.0553
Gnomad EAS
AF:
0.00160
Gnomad SAS
AF:
0.0378
Gnomad FIN
AF:
0.0621
Gnomad MID
AF:
0.0255
Gnomad NFE
AF:
0.0915
Gnomad OTH
AF:
0.0568
GnomAD4 exome
AF:
0.0826
AC:
102765
AN:
1243832
Hom.:
4841
AF XY:
0.0819
AC XY:
51380
AN XY:
627470
show subpopulations
Gnomad4 AFR exome
AF:
0.0129
Gnomad4 AMR exome
AF:
0.0275
Gnomad4 ASJ exome
AF:
0.0619
Gnomad4 EAS exome
AF:
0.000208
Gnomad4 SAS exome
AF:
0.0474
Gnomad4 FIN exome
AF:
0.0689
Gnomad4 NFE exome
AF:
0.0958
Gnomad4 OTH exome
AF:
0.0717
GnomAD4 genome
AF:
0.0577
AC:
8599
AN:
149110
Hom.:
330
Cov.:
32
AF XY:
0.0548
AC XY:
3975
AN XY:
72586
show subpopulations
Gnomad4 AFR
AF:
0.0172
Gnomad4 AMR
AF:
0.0385
Gnomad4 ASJ
AF:
0.0553
Gnomad4 EAS
AF:
0.00161
Gnomad4 SAS
AF:
0.0379
Gnomad4 FIN
AF:
0.0621
Gnomad4 NFE
AF:
0.0915
Gnomad4 OTH
AF:
0.0562
Alfa
AF:
0.0777
Hom.:
121
Bravo
AF:
0.0529
Asia WGS
AF:
0.0170
AC:
58
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 20, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.8
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs114060047; hg19: chr3-77090112; API