rs7704526

Variant names:

• chr5-169165144-T-C
• rs7704526
• NM_003062.4:c.413+28335A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-169165144-T-C
• chr5-169165144-T-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+28335A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,050 control chromosomes in the GnomAD database, including 10,072 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 0.36 (10072 hom., cov: 34)
• Consequence: SLIT3 NM_003062.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 0 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLIT3	NM_003062.4	c.413+28335A>G		intron_variant	Intron 4 of 35	ENST00000519560.6	NP_003053.2
SLIT3	NM_001271946.2	c.413+28335A>G		intron_variant	Intron 4 of 35		NP_001258875.2
SLIT3	XM_017009779.1	c.224+28335A>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+28335A>G		intron_variant	Intron 4 of 35	1	NM_003062.4	ENSP00000430333.2
SLIT3	ENST00000332966.8	c.413+28335A>G		intron_variant	Intron 4 of 35	1		ENSP00000332164.8
SLIT3	ENST00000518140.5	n.450+28335A>G		intron_variant	Intron 4 of 13	1
SLIT3	ENST00000521130.1	n.481+28335A>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54045 AN: 151932 Hom.: 10041 Cov.: 34

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.356 AC: 54141 AN: 152050 Hom.: 10072 Cov.: 34 AF XY: 0.358 AC XY: 26575 AN XY: 74326

African (AFR) AF: 0.431 AC: 17884 AN: 41480

American (AMR) AF: 0.408 AC: 6245 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2560 AN: 5174

South Asian (SAS) AF: 0.280 AC: 1344 AN: 4804

European-Finnish (FIN) AF: 0.303 AC: 3204 AN: 10564

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20534 AN: 67948

Other (OTH) AF: 0.346 AC: 731 AN: 2114

Alfa AF: 0.324 Hom.: 25588

Bravo AF: 0.367

Asia WGS AF: 0.394 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-0.96
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: rs7704526; hg19: chr5-168592148;