rs11713158

Variant names:

• chr3-2854000-T-C
• rs11713158
• NM_175607.3:c.455-12752T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-2854000-T-C
• chr3-2854000-T-G

Variant summary

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

The NM_175607.3(CNTN4):​c.455-12752T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,098 control chromosomes in the GnomAD database, including 47,745 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 0.79 (47745 hom., cov: 32)
• Consequence: CNTN4 NM_175607.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 6 publications found

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]

CNTN4 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• autism spectrum disorder

  Inheritance: AD Classification: NO_KNOWN Submitted by: Illumina

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN4	NM_175607.3	c.455-12752T>C		intron_variant	Intron 7 of 24	ENST00000418658.6	NP_783200.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN4	ENST00000418658.6	c.455-12752T>C		intron_variant	Intron 7 of 24	5	NM_175607.3	ENSP00000396010.1

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120363 AN: 151980 Hom.: 47703 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.792 AC: 120453 AN: 152098 Hom.: 47745 Cov.: 32 AF XY: 0.788 AC XY: 58572 AN XY: 74340

African (AFR) AF: 0.804 AC: 33350 AN: 41482

American (AMR) AF: 0.839 AC: 12818 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2812 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3395 AN: 5152

South Asian (SAS) AF: 0.827 AC: 3994 AN: 4828

European-Finnish (FIN) AF: 0.701 AC: 7408 AN: 10568

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54038 AN: 68000

Other (OTH) AF: 0.815 AC: 1722 AN: 2114

Alfa AF: 0.795 Hom.: 201501

Bravo AF: 0.802

Asia WGS AF: 0.742 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.040
DANN	Benign	0.36
PhyloP100		-1.8
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: rs11713158; hg19: chr3-2895684;