3-3042759-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_175607.3(CNTN4):​c.2512-218A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 605,162 control chromosomes in the GnomAD database, including 5,658 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2888 hom., cov: 33)
Exomes 𝑓: 0.096 ( 2770 hom. )

Consequence

CNTN4
NM_175607.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.683
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 3-3042759-A-T is Benign according to our data. Variant chr3-3042759-A-T is described in ClinVar as [Benign]. Clinvar id is 1287127.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CNTN4NM_175607.3 linkuse as main transcriptc.2512-218A>T intron_variant ENST00000418658.6 NP_783200.1 Q8IWV2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CNTN4ENST00000418658.6 linkuse as main transcriptc.2512-218A>T intron_variant 5 NM_175607.3 ENSP00000396010.1 Q8IWV2-1

Frequencies

GnomAD3 genomes
AF:
0.159
AC:
24143
AN:
152024
Hom.:
2871
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.334
Gnomad AMI
AF:
0.0636
Gnomad AMR
AF:
0.118
Gnomad ASJ
AF:
0.158
Gnomad EAS
AF:
0.00173
Gnomad SAS
AF:
0.0643
Gnomad FIN
AF:
0.0523
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.0982
Gnomad OTH
AF:
0.149
GnomAD4 exome
AF:
0.0961
AC:
43546
AN:
453020
Hom.:
2770
AF XY:
0.0947
AC XY:
22820
AN XY:
241028
show subpopulations
Gnomad4 AFR exome
AF:
0.336
Gnomad4 AMR exome
AF:
0.0911
Gnomad4 ASJ exome
AF:
0.178
Gnomad4 EAS exome
AF:
0.000484
Gnomad4 SAS exome
AF:
0.0721
Gnomad4 FIN exome
AF:
0.0541
Gnomad4 NFE exome
AF:
0.0989
Gnomad4 OTH exome
AF:
0.112
GnomAD4 genome
AF:
0.159
AC:
24193
AN:
152142
Hom.:
2888
Cov.:
33
AF XY:
0.153
AC XY:
11414
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.335
Gnomad4 AMR
AF:
0.118
Gnomad4 ASJ
AF:
0.158
Gnomad4 EAS
AF:
0.00173
Gnomad4 SAS
AF:
0.0648
Gnomad4 FIN
AF:
0.0523
Gnomad4 NFE
AF:
0.0982
Gnomad4 OTH
AF:
0.147
Alfa
AF:
0.137
Hom.:
252
Bravo
AF:
0.172
Asia WGS
AF:
0.0480
AC:
167
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
4.3
DANN
Benign
0.47

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: rs468314; hg19: chr3-3084443; API