rs6590474

Positions:

• chr11-99982441-A-C
• chr11-99982441-A-G
• chr11-99982441-A-T

Variant summary

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

The NM_014361.4(CNTN5):​c.878-19593A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 151,948 control chromosomes in the GnomAD database, including 39,009 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 0.71 (39009 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.878-19593A>C		intron_variant		ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.878-19593A>C		intron_variant		1	NM_014361.4	ENSP00000435637	P1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108124 AN: 151830 Hom.: 38974 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.712 AC: 108216 AN: 151948 Hom.: 39009 Cov.: 31 AF XY: 0.709 AC XY: 52673 AN XY: 74272

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.693

Alfa AF: 0.697 Hom.: 13096

Bravo AF: 0.729

Asia WGS AF: 0.684 AC: 2377 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	0.33
DANN	Benign	0.53

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: rs6590474; hg19: chr11-99853173;