rs3886342

Variant names:

• chr3-74600052-C-G
• rs3886342
• NM_020872.3:c.-81+14339G>C

Variant summary

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

The NM_020872.3(CNTN3):​c.-81+14339G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 151,798 control chromosomes in the GnomAD database, including 5,066 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 0.19 (5066 hom., cov: 32)
• Consequence: CNTN3 NM_020872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN3	NM_020872.3	c.-81+14339G>C		intron_variant	Intron 1 of 22	ENST00000263665.7	NP_065923.1
CNTN3	NM_001393376.1	c.-81+13696G>C		intron_variant	Intron 1 of 22		NP_001380305.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN3	ENST00000263665.7	c.-81+14339G>C		intron_variant	Intron 1 of 22	1	NM_020872.3	ENSP00000263665.6

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28990 AN: 151680 Hom.: 5047 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.191 AC: 29048 AN: 151798 Hom.: 5066 Cov.: 32 AF XY: 0.193 AC XY: 14336 AN XY: 74208

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.0660

Gnomad4 NFE AF: 0.0495

Gnomad4 OTH AF: 0.186

Alfa AF: 0.126 Hom.: 384

Bravo AF: 0.214

Asia WGS AF: 0.273 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.62
DANN	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3886342; hg19: chr3-74649203;