rs1479530

Positions:

• chr3-1358735-C-G
• chr3-1358735-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN6	NM_001289080.2	c.1492+6284C>G		intron_variant		ENST00000446702.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN6	ENST00000446702.7	c.1492+6284C>G		intron_variant		1	NM_001289080.2	P1
CNTN6	ENST00000350110.2	c.1492+6284C>G		intron_variant		1		P1
CNTN6	ENST00000397479.6	c.*1630+6284C>G		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.431

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.26

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: rs1479530; hg19: chr3-1400419;