NM_033401.5:c.391-28951C>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033401.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTNAP4	NM_033401.5	MANE Select	c.391-28951C>T		intron	N/A	NP_207837.2	Q9C0A0-1
	CNTNAP4	NM_001322181.2		c.388-28951C>T		intron	N/A	NP_001309110.1
	CNTNAP4	NM_001322188.2		c.391-28951C>T		intron	N/A	NP_001309117.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTNAP4	ENST00000611870.5	TSL:1 MANE Select	c.391-28951C>T		intron	N/A	ENSP00000479811.1	Q9C0A0-1
	CNTNAP4	ENST00000622250.4	TSL:1	c.391-28951C>T		intron	N/A	ENSP00000477698.1	A0A087WTA1
	CNTNAP4	ENST00000463177.1	TSL:1	n.333-28951C>T		intron	N/A

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

African (AFR) AF: 0.0825 AC: 3423 AN: 41504

American (AMR) AF: 0.156 AC: 2387 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1791 AN: 5132

South Asian (SAS) AF: 0.192 AC: 927 AN: 4818

European-Finnish (FIN) AF: 0.0527 AC: 559 AN: 10608

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0867 AC: 5896 AN: 67988

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.0971 Hom.: 1369

Bravo AF: 0.112

Asia WGS AF: 0.286 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.76
PhyloP100		-0.35
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: rs4887855; hg19: chr16-76432398;