rs4887855

Variant names:

• chr16-76398501-C-T
• rs4887855
• NM_033401.5:c.391-28951C>T

Variant summary

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

The NM_033401.5(CNTNAP4):​c.391-28951C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,116 control chromosomes in the GnomAD database, including 1,043 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 0.10 (1043 hom., cov: 30)
• Consequence: CNTNAP4 NM_033401.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

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]

ENSG00000287694 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTNAP4	NM_033401.5	c.391-28951C>T		intron_variant	Intron 3 of 23	ENST00000611870.5	NP_207837.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTNAP4	ENST00000611870.5	c.391-28951C>T		intron_variant	Intron 3 of 23	1	NM_033401.5	ENSP00000479811.1
ENSG00000287694	ENST00000655556.1	n.391-28951C>T		intron_variant	Intron 3 of 24			ENSP00000499374.1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15825 AN: 151998 Hom.: 1046 Cov.: 30

Gnomad AFR AF: 0.0826

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.104 AC: 15825 AN: 152116 Hom.: 1043 Cov.: 30 AF XY: 0.105 AC XY: 7838 AN XY: 74374

Gnomad4 AFR AF: 0.0825

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0867

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0933 Hom.: 835

Bravo AF: 0.112

Asia WGS AF: 0.286 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
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: rs4887855; hg19: chr16-76432398;