NM_175607.3:c.55+25904T>C

Variant names:

• chr3-2597462-T-C
• rs9819935
• NM_175607.3:c.55+25904T>C

Variant summary

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

The NM_175607.3(CNTN4):​c.55+25904T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,132 control chromosomes in the GnomAD database, including 2,818 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 0.14 (2818 hom., cov: 32)
• Consequence: CNTN4 NM_175607.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.735
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175607.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN4	NM_175607.3	MANE Select	c.55+25904T>C		intron	N/A	NP_783200.1
	CNTN4	NM_001206955.2		c.55+25904T>C		intron	N/A	NP_001193884.1
	CNTN4	NM_001350095.2		c.55+25904T>C		intron	N/A	NP_001337024.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN4	ENST00000418658.6	TSL:5 MANE Select	c.55+25904T>C		intron	N/A	ENSP00000396010.1
	CNTN4	ENST00000397461.5	TSL:5	c.55+25904T>C		intron	N/A	ENSP00000380602.1
	CNTN4	ENST00000427331.5	TSL:5	c.55+25904T>C		intron	N/A	ENSP00000413642.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21341 AN: 152014 Hom.: 2810 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.141 AC: 21398 AN: 152132 Hom.: 2818 Cov.: 32 AF XY: 0.137 AC XY: 10216 AN XY: 74384

African (AFR) AF: 0.335 AC: 13900 AN: 41466

American (AMR) AF: 0.182 AC: 2778 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0903 AC: 313 AN: 3466

East Asian (EAS) AF: 0.164 AC: 850 AN: 5170

South Asian (SAS) AF: 0.0836 AC: 403 AN: 4822

European-Finnish (FIN) AF: 0.0261 AC: 277 AN: 10614

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0382 AC: 2598 AN: 68004

Other (OTH) AF: 0.121 AC: 255 AN: 2108

Alfa AF: 0.0705 Hom.: 1703

Bravo AF: 0.165

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		0.73
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: rs9819935; hg19: chr3-2639146;