rs10516056

Variant names:

• chr5-169041532-C-T
• rs10516056
• NM_003062.4:c.413+151947G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLIT3	NM_003062.4	c.413+151947G>A		intron_variant	Intron 4 of 35	ENST00000519560.6	NP_003053.2
SLIT3	NM_001271946.2	c.413+151947G>A		intron_variant	Intron 4 of 35		NP_001258875.2
SLIT3	XM_017009779.1	c.224+151947G>A		intron_variant	Intron 4 of 35		XP_016865268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLIT3	ENST00000519560.6	c.413+151947G>A		intron_variant	Intron 4 of 35	1	NM_003062.4	ENSP00000430333.2
SLIT3	ENST00000332966.8	c.413+151947G>A		intron_variant	Intron 4 of 35	1		ENSP00000332164.8
SLIT3	ENST00000518140.5	n.450+151947G>A		intron_variant	Intron 4 of 13	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

African (AFR) AF: 0.0410 AC: 1705 AN: 41548

American (AMR) AF: 0.202 AC: 3090 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3468

East Asian (EAS) AF: 0.229 AC: 1184 AN: 5170

South Asian (SAS) AF: 0.344 AC: 1659 AN: 4818

European-Finnish (FIN) AF: 0.205 AC: 2174 AN: 10584

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14640 AN: 67982

Other (OTH) AF: 0.190 AC: 401 AN: 2112

Alfa AF: 0.210 Hom.: 4677

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
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10516056; hg19: chr5-168468537;