rs867477

chr5-168807986-C-A

Variant summary

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

The NM_003062.4(SLIT3):c.794-1399G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,152 control chromosomes in the GnomAD database, including 1,626 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 0.14 (1626 hom., cov: 32)
• Consequence: SLIT3 NM_003062.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLIT3	NM_003062.4	c.794-1399G>T		intron_variant		ENST00000519560.6
SLIT3	NM_001271946.2	c.794-1399G>T		intron_variant
SLIT3	XM_017009779.1	c.605-1399G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLIT3	ENST00000519560.6	c.794-1399G>T		intron_variant		1	NM_003062.4	A1
SLIT3	ENST00000332966.8	c.794-1399G>T		intron_variant		1		P4
SLIT3	ENST00000518140.5	n.831-1399G>T		intron_variant, non_coding_transcript_variant		1
SLIT3	ENST00000521150.1	n.486-1399G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20878 AN: 152034 Hom.: 1627 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.137 AC: 20874 AN: 152152 Hom.: 1626 Cov.: 32 AF XY: 0.135 AC XY: 10041 AN XY: 74388

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.0504

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.119

Alfa AF: 0.119 Hom.: 1269

Bravo AF: 0.141

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.6
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: rs867477; hg19: chr5-168234991; COSMIC: COSV60598789;