rs6564350

chr16-76547705-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_033401.5(CNTNAP4):c.3443-5578G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,054 control chromosomes in the GnomAD database, including 7,788 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 0.32 (7788 hom., cov: 32)
• Consequence: CNTNAP4 NM_033401.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673

Genes affected

CNTNAP4 (HGNC:18747): (contactin associated protein family member 4) This gene encodes a member of the neurexin protein family. Members of this family function in the vertebrate nervous system as cell adhesion molecules and receptors. This protein contains epidermal growth factor repeats and laminin G domains. In addition, it includes an F5/8 type C domain, discoidin/neuropilin- and fibrinogen-like domains, and thrombospondin N-terminal-like domains. This protein may also play a role in proper neurotransmission in the dopaminergic and GABAergic systems and mutations in this gene may be associated with certain psychiatric illnesses. A polymorphism in an intron of this gene may be associated with longevity. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTNAP4	NM_033401.5	c.3443-5578G>A		intron_variant		ENST00000611870.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTNAP4	ENST00000611870.5	c.3443-5578G>A		intron_variant		1	NM_033401.5	P4

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47891 AN: 151936 Hom.: 7773 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.315 AC: 47937 AN: 152054 Hom.: 7788 Cov.: 32 AF XY: 0.313 AC XY: 23254 AN XY: 74310

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.266

Alfa AF: 0.287 Hom.: 13126

Bravo AF: 0.314

Asia WGS AF: 0.391 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	13
Dann	Benign	0.82

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: rs6564350; hg19: chr16-76581602;