Variant 11-99168926-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_014361.4(CNTN5):c.-210+147656C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,072 control chromosomes in the GnomAD database, including 15,004 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 0.43 ( 15004 hom., cov: 33)

Consequence

CNTN5
NM_014361.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.361

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]

CNTN5 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN5	NM_014361.4 link	c.-210+147656C>T		intron_variant		ENST00000524871.6	NP_055176.1	O94779-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CNTN5	ENST00000524871.6 link	c.-210+147656C>T	intron_variant	1	NM_014361.4	ENSP00000435637.1	O94779-1
CNTN5	ENST00000527185.5 link	c.-210+147656C>T	intron_variant	1		ENSP00000433575.1	O94779-4
CNTN5	ENST00000528727.5 link	n.295+147656C>T	intron_variant	1
CNTN5	ENST00000528682.5 link	c.-71+147656C>T	intron_variant	5		ENSP00000436185.1	O94779-1

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65537

AN:

151954

Hom.:

14992

Cov.:

show subpopulations

Gnomad AFR

AF:

0.317

Gnomad AMI

AF:

0.394

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.430

Gnomad EAS

AF:

0.805

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.434

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

GnomAD4 genome

AF:

0.431

AC:

65579

AN:

152072

Hom.:

15004

Cov.:

AF XY:

0.441

AC XY:

32769

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.317

Gnomad4 AMR

AF:

0.511

Gnomad4 ASJ

AF:

0.430

Gnomad4 EAS

AF:

0.805

Gnomad4 SAS

AF:

0.524

Gnomad4 FIN

AF:

0.503

Gnomad4 NFE

AF:

0.437

Gnomad4 OTH

AF:

0.438

Alfa

AF:

0.347

Hom.:

1643

Bravo

AF:

0.425

Asia WGS

AF:

0.621

AC:

2158

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.8

DANN

Benign

0.66

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over