rs9876789

Positions:

• chr3-74496729-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020872.3(CNTN3):​c.182+2930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,068 control chromosomes in the GnomAD database, including 1,290 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 0.12 (1290 hom., cov: 32)
• Consequence: CNTN3 NM_020872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN3	NM_020872.3	c.182+2930C>T		intron_variant		ENST00000263665.7
CNTN3	NM_001393376.1	c.182+2930C>T		intron_variant
CNTN3	XM_011533768.3	c.182+2930C>T		intron_variant
CNTN3	XM_017006508.2	c.-43+2930C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN3	ENST00000263665.7	c.182+2930C>T		intron_variant		1	NM_020872.3	P1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17467 AN: 151950 Hom.: 1282 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0604

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.115 AC: 17519 AN: 152068 Hom.: 1290 Cov.: 32 AF XY: 0.115 AC XY: 8524 AN XY: 74338

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0604

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0886 Hom.: 386

Bravo AF: 0.124

Asia WGS AF: 0.193 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	14
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9876789; hg19: chr3-74545880;