chr3-1358735-C-G

Variant names:

• chr3-1358735-C-G
• rs1479530
• NM_001289080.2:c.1492+6284C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001289080.2(CNTN6):​c.1492+6284C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,746 control chromosomes in the GnomAD database, including 18,325 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 0.46 (18325 hom., cov: 32)
• Consequence: CNTN6 NM_001289080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769
• Publications: 5 publications found

Genes affected

CNTN6 (HGNC:2176): (contactin 6) The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

CNTN6 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
• complex neurodevelopmental disorder

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001289080.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN6	NM_001289080.2	MANE Select	c.1492+6284C>G		intron	N/A	NP_001276009.1	Q9UQ52
	CNTN6	NM_001349350.2		c.1492+6284C>G		intron	N/A	NP_001336279.1	Q9UQ52
	CNTN6	NM_001349351.2		c.1492+6284C>G		intron	N/A	NP_001336280.1	Q9UQ52

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN6	ENST00000446702.7	TSL:1 MANE Select	c.1492+6284C>G		intron	N/A	ENSP00000407822.2	Q9UQ52
	CNTN6	ENST00000350110.2	TSL:1	c.1492+6284C>G		intron	N/A	ENSP00000341882.2	Q9UQ52
	CNTN6	ENST00000861157.1		c.1492+6284C>G		intron	N/A	ENSP00000531216.1

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69539 AN: 151628 Hom.: 18297 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.459 AC: 69606 AN: 151746 Hom.: 18325 Cov.: 32 AF XY: 0.456 AC XY: 33783 AN XY: 74130

African (AFR) AF: 0.715 AC: 29617 AN: 41398

American (AMR) AF: 0.318 AC: 4828 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1333 AN: 3466

East Asian (EAS) AF: 0.101 AC: 519 AN: 5126

South Asian (SAS) AF: 0.225 AC: 1083 AN: 4814

European-Finnish (FIN) AF: 0.527 AC: 5555 AN: 10546

Middle Eastern (MID) AF: 0.441 AC: 127 AN: 288

European-Non Finnish (NFE) AF: 0.372 AC: 25291 AN: 67902

Other (OTH) AF: 0.431 AC: 911 AN: 2112

Alfa AF: 0.261 Hom.: 601

Bravo AF: 0.455

Asia WGS AF: 0.204 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.26
PhyloP100		-0.77
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: rs1479530; hg19: chr3-1400419;