5-168814958-T-C

Variant names:

• chr5-168814958-T-C
• rs9885172
• NM_003062.4:c.793+2342A>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.793+2342A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,918 control chromosomes in the GnomAD database, including 22,088 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 0.53 (22088 hom., cov: 31)
• Consequence: SLIT3 NM_003062.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLIT3	NM_003062.4	c.793+2342A>G		intron_variant	Intron 8 of 35	ENST00000519560.6	NP_003053.2
SLIT3	NM_001271946.2	c.793+2342A>G		intron_variant	Intron 8 of 35		NP_001258875.2
SLIT3	XM_017009779.1	c.604+2342A>G		intron_variant	Intron 8 of 35		XP_016865268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLIT3	ENST00000519560.6	c.793+2342A>G		intron_variant	Intron 8 of 35	1	NM_003062.4	ENSP00000430333.2
SLIT3	ENST00000332966.8	c.793+2342A>G		intron_variant	Intron 8 of 35	1		ENSP00000332164.8
SLIT3	ENST00000518140.5	n.830+2342A>G		intron_variant	Intron 8 of 13	1
SLIT3	ENST00000521150.1	n.485+2342A>G		intron_variant	Intron 3 of 7	2

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81090 AN: 151796 Hom.: 22053 Cov.: 31

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.534 AC: 81175 AN: 151918 Hom.: 22088 Cov.: 31 AF XY: 0.532 AC XY: 39473 AN XY: 74226

African (AFR) AF: 0.617 AC: 25585 AN: 41450

American (AMR) AF: 0.489 AC: 7460 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1989 AN: 3464

East Asian (EAS) AF: 0.590 AC: 3039 AN: 5152

South Asian (SAS) AF: 0.575 AC: 2763 AN: 4802

European-Finnish (FIN) AF: 0.430 AC: 4536 AN: 10546

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34044 AN: 67928

Other (OTH) AF: 0.539 AC: 1137 AN: 2110

Alfa AF: 0.510 Hom.: 11667

Bravo AF: 0.543

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.33
PhyloP100		-0.82
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: rs9885172; hg19: chr5-168241963;