rs297808

chr5-169123560-T-C

Variant summary

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

The NM_003062.4(SLIT3):c.413+69919A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,034 control chromosomes in the GnomAD database, including 8,831 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 0.34 (8831 hom., cov: 33)
• Consequence: SLIT3 NM_003062.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLIT3	NM_003062.4	c.413+69919A>G		intron_variant		ENST00000519560.6
SLIT3	NM_001271946.2	c.413+69919A>G		intron_variant
SLIT3	XM_017009779.1	c.224+69919A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLIT3	ENST00000519560.6	c.413+69919A>G		intron_variant		1	NM_003062.4	A1
SLIT3	ENST00000332966.8	c.413+69919A>G		intron_variant		1		P4
SLIT3	ENST00000518140.5	n.450+69919A>G		intron_variant, non_coding_transcript_variant		1
SLIT3	ENST00000521130.1	n.482-3199A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51457 AN: 151916 Hom.: 8824 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.339 AC: 51472 AN: 152034 Hom.: 8831 Cov.: 33 AF XY: 0.337 AC XY: 25042 AN XY: 74300

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.314

Alfa AF: 0.336 Hom.: 17628

Bravo AF: 0.332

Asia WGS AF: 0.357 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.9
Dann	Benign	0.71

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: rs297808; hg19: chr5-168550565;