rs7652782

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_175607.3(CNTN4):​c.358+34235G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,152 control chromosomes in the GnomAD database, including 1,813 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 0.15 ( 1813 hom., cov: 33)

Consequence

CNTN4
NM_175607.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.286
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CNTN4NM_175607.3 linkuse as main transcriptc.358+34235G>A intron_variant ENST00000418658.6 NP_783200.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CNTN4ENST00000418658.6 linkuse as main transcriptc.358+34235G>A intron_variant 5 NM_175607.3 ENSP00000396010 P1Q8IWV2-1

Frequencies

GnomAD3 genomes
AF:
0.146
AC:
22213
AN:
152034
Hom.:
1804
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.212
Gnomad AMI
AF:
0.0824
Gnomad AMR
AF:
0.0854
Gnomad ASJ
AF:
0.0807
Gnomad EAS
AF:
0.131
Gnomad SAS
AF:
0.141
Gnomad FIN
AF:
0.171
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.122
Gnomad OTH
AF:
0.139
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.146
AC:
22257
AN:
152152
Hom.:
1813
Cov.:
33
AF XY:
0.146
AC XY:
10894
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.213
Gnomad4 AMR
AF:
0.0852
Gnomad4 ASJ
AF:
0.0807
Gnomad4 EAS
AF:
0.132
Gnomad4 SAS
AF:
0.141
Gnomad4 FIN
AF:
0.171
Gnomad4 NFE
AF:
0.122
Gnomad4 OTH
AF:
0.139
Alfa
AF:
0.115
Hom.:
592
Bravo
AF:
0.142
Asia WGS
AF:
0.146
AC:
506
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
3.2
DANN
Benign
0.69

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7652782; hg19: chr3-2821616; API