rs17024684

chr3-3013563-C-T

Variant summary

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

The NM_175607.3(CNTN4):c.1487-12539C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,000 control chromosomes in the GnomAD database, including 547 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 0.077 (547 hom., cov: 32)
• Consequence: CNTN4 NM_175607.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

CNTN4 (HGNC:2174): (contactin 4) This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN4	NM_175607.3	c.1487-12539C>T		intron_variant		ENST00000418658.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN4	ENST00000418658.6	c.1487-12539C>T		intron_variant		5	NM_175607.3	P1

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 11733 AN: 151882 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0877

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0771 AC: 11717 AN: 152000 Hom.: 547 Cov.: 32 AF XY: 0.0785 AC XY: 5828 AN XY: 74264

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0703

Gnomad4 NFE AF: 0.0877

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0828 Hom.: 380

Bravo AF: 0.0804

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.3
Dann	Benign	0.76

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: rs17024684; hg19: chr3-3055247;