rs6590484

Positions:

• chr11-99987223-T-C

Variant summary

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

The NM_014361.4(CNTN5):​c.878-14811T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,772 control chromosomes in the GnomAD database, including 15,092 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 (15092 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN5	NM_014361.4	c.878-14811T>C		intron_variant		ENST00000524871.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN5	ENST00000524871.6	c.878-14811T>C		intron_variant		1	NM_014361.4	P1

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65136 AN: 151654 Hom.: 15077 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.430 AC: 65191 AN: 151772 Hom.: 15092 Cov.: 31 AF XY: 0.422 AC XY: 31288 AN XY: 74136

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.412

Alfa AF: 0.395 Hom.: 5720

Bravo AF: 0.440

Asia WGS AF: 0.288 AC: 1003 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.8
DANN	Benign	0.54

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: rs6590484; hg19: chr11-99857955;