rs1472025

Variant names:

• chr3-1129960-C-A
• rs1472025
• NM_001289080.2:c.-82-17967C>A

Variant summary

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

The NM_001289080.2(CNTN6):​c.-82-17967C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,944 control chromosomes in the GnomAD database, including 5,896 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 0.25 (5896 hom., cov: 33)
• Consequence: CNTN6 NM_001289080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 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.-82-17967C>A		intron	N/A	NP_001276009.1	Q9UQ52
	CNTN6	NM_001349350.2		c.-83+1583C>A		intron	N/A	NP_001336279.1	Q9UQ52
	CNTN6	NM_001349351.2		c.-83+1583C>A		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.-82-17967C>A		intron	N/A	ENSP00000407822.2	Q9UQ52
	CNTN6	ENST00000350110.2	TSL:1	c.-82-17967C>A		intron	N/A	ENSP00000341882.2	Q9UQ52
	CNTN6	ENST00000394261.2	TSL:1	n.-93-17967C>A		intron	N/A	ENSP00000377804.2	F8WDQ0

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37788 AN: 151826 Hom.: 5872 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.249 AC: 37854 AN: 151944 Hom.: 5896 Cov.: 33 AF XY: 0.245 AC XY: 18218 AN XY: 74242

African (AFR) AF: 0.438 AC: 18158 AN: 41430

American (AMR) AF: 0.201 AC: 3052 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3470

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5168

South Asian (SAS) AF: 0.146 AC: 704 AN: 4812

European-Finnish (FIN) AF: 0.171 AC: 1813 AN: 10574

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12311 AN: 67960

Other (OTH) AF: 0.238 AC: 500 AN: 2104

Alfa AF: 0.226 Hom.: 568

Bravo AF: 0.261

Asia WGS AF: 0.101 AC: 352 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.058
DANN	Benign	0.17
PhyloP100		-1.4
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: rs1472025; hg19: chr3-1171644;