chr11-99071142-A-G

Position:

• chr11-99071142-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014361.4(CNTN5):​c.-210+49872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,848 control chromosomes in the GnomAD database, including 11,537 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 0.39 (11537 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.-210+49872A>G		intron_variant		ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.-210+49872A>G		intron_variant		1	NM_014361.4	ENSP00000435637.1
CNTN5	ENST00000527185.5	c.-210+49872A>G		intron_variant		1		ENSP00000433575.1
CNTN5	ENST00000528727.5	n.295+49872A>G		intron_variant		1
CNTN5	ENST00000528682.5	c.-71+49872A>G		intron_variant		5		ENSP00000436185.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58448 AN: 151732 Hom.: 11520 Cov.: 31

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.385 AC: 58501 AN: 151848 Hom.: 11537 Cov.: 31 AF XY: 0.390 AC XY: 28937 AN XY: 74214

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.412

Alfa AF: 0.349 Hom.: 19413

Bravo AF: 0.394

Asia WGS AF: 0.533 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.033
DANN	Benign	0.42

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

Other links and lift over

dbSNP: rs1940484; hg19: chr11-98941872;