rs1472025

chr3-1129960-C-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN6	NM_001289080.2	c.-82-17967C>A		intron_variant		ENST00000446702.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN6	ENST00000446702.7	c.-82-17967C>A		intron_variant		1	NM_001289080.2	P1

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

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0203

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.238

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.058
Dann	Benign	0.17

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

Other links and lift over

dbSNP: rs1472025; hg19: chr3-1171644;