Variant 5-168671230-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_003062.4(SLIT3):c.4095T>C(p.Asp1365=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,611,118 control chromosomes in the GnomAD database, including 55,305 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.31 ( 7948 hom., cov: 33)

Exomes 𝑓: 0.25 ( 47357 hom. )

Consequence

SLIT3
NM_003062.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.52

Variant links:

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]

SLIT3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 5-168671230-A-G is Benign according to our data. Variant chr5-168671230-A-G is described in ClinVar as [Benign]. Clinvar id is 1268560.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=3.52 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLIT3	NM_003062.4 linkuse as main transcript	c.4095T>C	p.Asp1365=	synonymous_variant	34/36	ENST00000519560.6	NP_003053.2
SLIT3	NM_001271946.2 linkuse as main transcript	c.4116T>C	p.Asp1372=	synonymous_variant	34/36		NP_001258875.2
SLIT3	XM_017009779.1 linkuse as main transcript	c.3906T>C	p.Asp1302=	synonymous_variant	34/36		XP_016865268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLIT3	ENST00000519560.6 linkuse as main transcript	c.4095T>C	p.Asp1365=	synonymous_variant	34/36	1	NM_003062.4	ENSP00000430333	A1	O75094-1
SLIT3	ENST00000332966.8 linkuse as main transcript	c.4116T>C	p.Asp1372=	synonymous_variant	34/36	1		ENSP00000332164	P4	O75094-4

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47052

AN:

151996

Hom.:

7924

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.362

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.270

GnomAD3 exomes

AF:

0.272

AC:

66878

AN:

245816

Hom.:

10143

AF XY:

0.256

AC XY:

34230

AN XY:

133664

show subpopulations

Gnomad AFR exome

AF:

0.443

Gnomad AMR exome

AF:

0.414

Gnomad ASJ exome

AF:

0.162

Gnomad EAS exome

AF:

0.324

Gnomad SAS exome

AF:

0.149

Gnomad FIN exome

AF:

0.302

Gnomad NFE exome

AF:

0.235

Gnomad OTH exome

AF:

0.244

GnomAD4 exome

AF:

0.248

AC:

362381

AN:

1459004

Hom.:

47357

Cov.:

AF XY:

0.244

AC XY:

176775

AN XY:

725452

show subpopulations

Gnomad4 AFR exome

AF:

0.438

Gnomad4 AMR exome

AF:

0.407

Gnomad4 ASJ exome

AF:

0.161

Gnomad4 EAS exome

AF:

0.347

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.301

Gnomad4 NFE exome

AF:

0.241

Gnomad4 OTH exome

AF:

0.247

GnomAD4 genome

AF:

0.310

AC:

47135

AN:

152114

Hom.:

7948

Cov.:

AF XY:

0.313

AC XY:

23290

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.437

Gnomad4 AMR

AF:

0.362

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.300

Gnomad4 NFE

AF:

0.241

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.249

Hom.:

1622

Bravo

AF:

0.322

Asia WGS

AF:

0.232

AC:

810

AN:

3478

EpiCase

AF:

0.211

EpiControl

AF:

0.218

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

3.3

DANN

Benign

0.54

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over