rs4282339

chr5-168829235-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_003062.4(SLIT3):c.558-5904C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,234 control chromosomes in the GnomAD database, including 2,856 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 0.19 (2856 hom., cov: 32)
• Consequence: SLIT3 NM_003062.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

SLIT3 (HGNC:11087): (slit guidance ligand 3) The protein encoded by this gene is secreted, likely interacting with roundabout homolog receptors to effect cell migration. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLIT3	NM_003062.4	c.558-5904C>T		intron_variant		ENST00000519560.6
SLIT3	NM_001271946.2	c.558-5904C>T		intron_variant
SLIT3	XM_017009779.1	c.369-5904C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLIT3	ENST00000519560.6	c.558-5904C>T		intron_variant		1	NM_003062.4	A1
SLIT3	ENST00000332966.8	c.558-5904C>T		intron_variant		1		P4
SLIT3	ENST00000518140.5	n.595-5904C>T		intron_variant, non_coding_transcript_variant		1
SLIT3	ENST00000521150.1	n.250-5904C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28355 AN: 152116 Hom.: 2855 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.186 AC: 28372 AN: 152234 Hom.: 2856 Cov.: 32 AF XY: 0.188 AC XY: 14008 AN XY: 74452

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.189

Alfa AF: 0.205 Hom.: 7705

Bravo AF: 0.179

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
Cadd	Benign	19
Dann	Benign	0.75

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: rs4282339; hg19: chr5-168256240;