NM_003062.4:c.794-1399G>T

Variant names:

• chr5-168807986-C-A
• rs867477
• NM_003062.4:c.794-1399G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003062.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLIT3	NM_003062.4	MANE Select	c.794-1399G>T		intron	N/A	NP_003053.2
	SLIT3	NM_001271946.2		c.794-1399G>T		intron	N/A	NP_001258875.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLIT3	ENST00000519560.6	TSL:1 MANE Select	c.794-1399G>T		intron	N/A	ENSP00000430333.2
	SLIT3	ENST00000332966.8	TSL:1	c.794-1399G>T		intron	N/A	ENSP00000332164.8
	SLIT3	ENST00000518140.5	TSL:1	n.831-1399G>T		intron	N/A

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

African (AFR) AF: 0.213 AC: 8838 AN: 41506

American (AMR) AF: 0.107 AC: 1628 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3470

East Asian (EAS) AF: 0.0504 AC: 260 AN: 5160

South Asian (SAS) AF: 0.143 AC: 690 AN: 4816

European-Finnish (FIN) AF: 0.0961 AC: 1019 AN: 10606

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7717 AN: 68000

Other (OTH) AF: 0.119 AC: 251 AN: 2108

Alfa AF: 0.121 Hom.: 1685

Bravo AF: 0.141

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.71
PhyloP100		0.18
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: rs867477; hg19: chr5-168234991; COSMIC: COSV60598789;