rs1353825

Variant names:

• chr3-1296575-G-A
• rs1353825
• NM_001289080.2:c.658+771G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-1296575-G-A
• chr3-1296575-G-C
• chr3-1296575-G-T

Variant summary

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

The NM_001289080.2(CNTN6):​c.658+771G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,996 control chromosomes in the GnomAD database, including 3,881 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 0.22 (3881 hom., cov: 32)
• Consequence: CNTN6 NM_001289080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN6	NM_001289080.2	c.658+771G>A		intron_variant	Intron 6 of 22	ENST00000446702.7	NP_001276009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN6	ENST00000446702.7	c.658+771G>A		intron_variant	Intron 6 of 22	1	NM_001289080.2	ENSP00000407822.2
CNTN6	ENST00000350110.2	c.658+771G>A		intron_variant	Intron 6 of 22	1		ENSP00000341882.2
CNTN6	ENST00000394261.2	n.*636+771G>A		intron_variant	Intron 7 of 7	1		ENSP00000377804.2
CNTN6	ENST00000397479.6	n.*796+771G>A		intron_variant	Intron 5 of 21	2		ENSP00000380616.2

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33712 AN: 151878 Hom.: 3881 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.222 AC: 33730 AN: 151996 Hom.: 3881 Cov.: 32 AF XY: 0.215 AC XY: 15962 AN XY: 74288

African (AFR) AF: 0.198 AC: 8217 AN: 41464

American (AMR) AF: 0.190 AC: 2898 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1083 AN: 5166

South Asian (SAS) AF: 0.111 AC: 534 AN: 4822

European-Finnish (FIN) AF: 0.167 AC: 1758 AN: 10556

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.259 AC: 17578 AN: 67946

Other (OTH) AF: 0.223 AC: 470 AN: 2106

Alfa AF: 0.245 Hom.: 14882

Bravo AF: 0.226

Asia WGS AF: 0.156 AC: 545 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.029
DANN	Benign	0.47
PhyloP100		-1.3
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: rs1353825; hg19: chr3-1338259;