11-99975575-A-G

Variant summary

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

The NM_014361.4(CNTN5):​c.877+18566A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 151,994 control chromosomes in the GnomAD database, including 41,736 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 0.73 ( 41736 hom., cov: 31)

Consequence

CNTN5
NM_014361.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.574
Variant links:
Genes affected
CNTN5 (HGNC:2175): (contactin 5) The protein encoded by this gene is a member of the immunoglobulin superfamily, and contactin family, which mediate cell surface interactions during nervous system development. This protein is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CNTN5NM_014361.4 linkuse as main transcriptc.877+18566A>G intron_variant ENST00000524871.6 NP_055176.1 O94779-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CNTN5ENST00000524871.6 linkuse as main transcriptc.877+18566A>G intron_variant 1 NM_014361.4 ENSP00000435637.1 O94779-1

Frequencies

GnomAD3 genomes
AF:
0.734
AC:
111546
AN:
151876
Hom.:
41691
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.872
Gnomad AMI
AF:
0.747
Gnomad AMR
AF:
0.753
Gnomad ASJ
AF:
0.749
Gnomad EAS
AF:
0.804
Gnomad SAS
AF:
0.643
Gnomad FIN
AF:
0.631
Gnomad MID
AF:
0.725
Gnomad NFE
AF:
0.663
Gnomad OTH
AF:
0.729
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.735
AC:
111647
AN:
151994
Hom.:
41736
Cov.:
31
AF XY:
0.730
AC XY:
54249
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.872
Gnomad4 AMR
AF:
0.753
Gnomad4 ASJ
AF:
0.749
Gnomad4 EAS
AF:
0.804
Gnomad4 SAS
AF:
0.641
Gnomad4 FIN
AF:
0.631
Gnomad4 NFE
AF:
0.663
Gnomad4 OTH
AF:
0.727
Alfa
AF:
0.674
Hom.:
3193
Bravo
AF:
0.755
Asia WGS
AF:
0.685
AC:
2381
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.0
DANN
Benign
0.27

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: rs7103510; hg19: chr11-99846307; API