rs4076052

chr3-74492129-C-Achr3-74492129-C-G

Variant summary

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

The NM_020872.3(CNTN3):c.183-5498G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 152,230 control chromosomes in the GnomAD database, including 45 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 0.022 (45 hom., cov: 33)
• Consequence: CNTN3 NM_020872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

CNTN3 (HGNC:2173): (contactin 3) Predicted to be involved in cell adhesion and nervous system development. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in neuron projection. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN3	NM_020872.3	c.183-5498G>T		intron_variant		ENST00000263665.7
CNTN3	NM_001393376.1	c.183-5498G>T		intron_variant
CNTN3	XM_011533768.3	c.183-5498G>T		intron_variant
CNTN3	XM_017006508.2	c.8+883G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN3	ENST00000263665.7	c.183-5498G>T		intron_variant		1	NM_020872.3	P1

Frequencies

GnomAD3 genomes AF: 0.0221 AC: 3360 AN: 152112 Hom.: 44 Cov.: 33

Gnomad AFR AF: 0.00449

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0715

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0312

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0221 AC: 3367 AN: 152230 Hom.: 45 Cov.: 33 AF XY: 0.0221 AC XY: 1647 AN XY: 74436

Gnomad4 AFR AF: 0.00448

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0160

Gnomad4 SAS AF: 0.0714

Gnomad4 FIN AF: 0.0224

Gnomad4 NFE AF: 0.0312

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0191 Hom.: 16

Bravo AF: 0.0188

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	8.3
Dann	Benign	0.63

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: rs4076052; hg19: chr3-74541280;