NM_003062.4:c.413+69919A>G

Variant names:

• chr5-169123560-T-C
• rs297808
• NM_003062.4:c.413+69919A>G

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+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
• Publications: 1 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]

ENSG00000302955 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLIT3	NM_003062.4	c.413+69919A>G		intron_variant	Intron 4 of 35	ENST00000519560.6	NP_003053.2
SLIT3	NM_001271946.2	c.413+69919A>G		intron_variant	Intron 4 of 35		NP_001258875.2
SLIT3	XM_017009779.1	c.224+69919A>G		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+69919A>G		intron_variant	Intron 4 of 35	1	NM_003062.4	ENSP00000430333.2

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

African (AFR) AF: 0.329 AC: 13646 AN: 41468

American (AMR) AF: 0.307 AC: 4696 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2313 AN: 5184

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4810

European-Finnish (FIN) AF: 0.376 AC: 3964 AN: 10536

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23474 AN: 67978

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.338 Hom.: 36865

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
PhyloP100		0.31
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: rs297808; hg19: chr5-168550565;