rs1455824

Positions:

• chr3-79088080-G-A

Variant summary

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

The NM_002941.4(ROBO1):​c.172+37376C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,970 control chromosomes in the GnomAD database, including 4,097 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 0.23 (4097 hom., cov: 32)
• Consequence: ROBO1 NM_002941.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767

Genes affected

ROBO1 (HGNC:10249): (roundabout guidance receptor 1) Bilateral symmetric nervous systems have special midline structures that establish a partition between the two mirror image halves. Some axons project toward and across the midline in response to long-range chemoattractants emanating from the midline. The product of this gene is a member of the immunoglobulin gene superfamily and encodes an integral membrane protein that functions in axon guidance and neuronal precursor cell migration. This receptor is activated by SLIT-family proteins, resulting in a repulsive effect on glioma cell guidance in the developing brain. A related gene is located at an adjacent region on chromosome 3. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ROBO1	NM_002941.4	c.172+37376C>T		intron_variant		ENST00000464233.6	NP_002932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ROBO1	ENST00000464233.6	c.172+37376C>T		intron_variant		5	NM_002941.4	ENSP00000420321.1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34678 AN: 151852 Hom.: 4093 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.228 AC: 34691 AN: 151970 Hom.: 4097 Cov.: 32 AF XY: 0.228 AC XY: 16944 AN XY: 74276

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.224

Alfa AF: 0.258 Hom.: 9474

Bravo AF: 0.221

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1455824; hg19: chr3-79137230;