3-77040548-T-G

Variant names:

• chr3-77040548-T-G
• rs3923744
• NM_001395656.1:c.-238T>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001395656.1(ROBO2):​c.-238T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,395,666 control chromosomes in the GnomAD database, including 24,063 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.16 (2264 hom., cov: 32)
  • Exomes 𝑓: 0.18 (21799 hom.)
• Consequence: ROBO2 NM_001395656.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.102

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]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 3-77040548-T-G is Benign according to our data. Variant chr3-77040548-T-G is described in ClinVar as [Benign]. Clinvar id is 346671.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ROBO2	NM_001395656.1	c.-238T>G		5_prime_UTR_variant	Exon 1 of 28	ENST00000696593.1	NP_001382585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ROBO2	ENST00000696593.1	c.-238T>G		5_prime_UTR_variant	Exon 1 of 28		NM_001395656.1	ENSP00000512738.1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24965 AN: 151886 Hom.: 2255 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.155

GnomAD4 exome AF: 0.184 AC: 228404 AN: 1243664 Hom.: 21799 Cov.: 34 AF XY: 0.183 AC XY: 110465 AN XY: 602864

African (AFR) AF: 0.0985 AC: 2698 AN: 27392

American (AMR) AF: 0.277 AC: 4943 AN: 17852

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 2207 AN: 17554

East Asian (EAS) AF: 0.245 AC: 7729 AN: 31554

South Asian (SAS) AF: 0.193 AC: 11441 AN: 59388

European-Finnish (FIN) AF: 0.146 AC: 3660 AN: 24998

Middle Eastern (MID) AF: 0.143 AC: 483 AN: 3388

European-Non Finnish (NFE) AF: 0.184 AC: 185925 AN: 1010514

Other (OTH) AF: 0.183 AC: 9318 AN: 51024

GnomAD4 genome AF: 0.165 AC: 25011 AN: 152002 Hom.: 2264 Cov.: 32 AF XY: 0.169 AC XY: 12528 AN XY: 74318

African (AFR) AF: 0.104 AC: 4309 AN: 41456

American (AMR) AF: 0.252 AC: 3843 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1219 AN: 5124

South Asian (SAS) AF: 0.198 AC: 954 AN: 4812

European-Finnish (FIN) AF: 0.149 AC: 1583 AN: 10596

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12121 AN: 67954

Other (OTH) AF: 0.156 AC: 329 AN: 2106

Alfa AF: 0.168 Hom.: 2750

Bravo AF: 0.168

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Vesicoureteral reflux 2 Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	8.6
DANN	Benign	0.78
PhyloP100		-0.10
PromoterAI		-0.023	Neutral

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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Other links and lift over

dbSNP: rs3923744; hg19: chr3-77089699;