rs6797539

Positions:

• chr3-1105517-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001289080.2(CNTN6):​c.-83+12397A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 152,252 control chromosomes in the GnomAD database, including 423 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 0.065 (423 hom., cov: 33)
• Consequence: CNTN6 NM_001289080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.07

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN6	NM_001289080.2	c.-83+12397A>G		intron_variant		ENST00000446702.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN6	ENST00000446702.7	c.-83+12397A>G		intron_variant		1	NM_001289080.2	P1

Frequencies

GnomAD3 genomes AF: 0.0646 AC: 9830 AN: 152134 Hom.: 423 Cov.: 33

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.0809

Gnomad FIN AF: 0.0966

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0646 AC: 9839 AN: 152252 Hom.: 423 Cov.: 33 AF XY: 0.0660 AC XY: 4914 AN XY: 74444

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.00540

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.0966

Gnomad4 NFE AF: 0.0892

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0860 Hom.: 277

Bravo AF: 0.0583

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.058
DANN	Benign	0.34

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: rs6797539; hg19: chr3-1147201;