rs10516056

chr5-169041532-C-T

Variant summary

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

The NM_003062.4(SLIT3):c.413+151947G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,164 control chromosomes in the GnomAD database, including 2,807 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 0.17 (2807 hom., cov: 32)
• Consequence: SLIT3 NM_003062.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLIT3	NM_003062.4	c.413+151947G>A		intron_variant		ENST00000519560.6
SLIT3	NM_001271946.2	c.413+151947G>A		intron_variant
SLIT3	XM_017009779.1	c.224+151947G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLIT3	ENST00000519560.6	c.413+151947G>A		intron_variant		1	NM_003062.4	A1
SLIT3	ENST00000332966.8	c.413+151947G>A		intron_variant		1		P4
SLIT3	ENST00000518140.5	n.450+151947G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26022 AN: 152044 Hom.: 2799 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.171 AC: 26035 AN: 152164 Hom.: 2807 Cov.: 32 AF XY: 0.173 AC XY: 12897 AN XY: 74380

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.190

Alfa AF: 0.217 Hom.: 3795

Bravo AF: 0.165

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.96
Dann	Benign	0.77

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: rs10516056; hg19: chr5-168468537;