rs12803066

Positions:

• chr11-100172688-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.1581-18438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,020 control chromosomes in the GnomAD database, including 1,797 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 0.15 (1797 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.1581-18438A>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.1581-18438A>G		intron_variant		1	NM_014361.4	ENSP00000435637	P1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23399 AN: 151900 Hom.: 1796 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0914

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.154 AC: 23420 AN: 152020 Hom.: 1797 Cov.: 32 AF XY: 0.153 AC XY: 11376 AN XY: 74294

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.149

Alfa AF: 0.155 Hom.: 2561

Bravo AF: 0.149

Asia WGS AF: 0.142 AC: 494 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	0.46
DANN	Benign	0.33

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: rs12803066; hg19: chr11-100043420;