rs13073838

Positions:

• chr3-74578552-T-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+35839A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,928 control chromosomes in the GnomAD database, including 6,770 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 0.27 (6770 hom., cov: 32)
• Consequence: CNTN3 NM_020872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN3	NM_020872.3	c.-81+35839A>G		intron_variant		ENST00000263665.7	NP_065923.1
CNTN3	NM_001393376.1	c.-81+35196A>G		intron_variant			NP_001380305.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN3	ENST00000263665.7	c.-81+35839A>G		intron_variant		1	NM_020872.3	ENSP00000263665.6

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40717 AN: 151810 Hom.: 6771 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.268 AC: 40714 AN: 151928 Hom.: 6770 Cov.: 32 AF XY: 0.263 AC XY: 19527 AN XY: 74240

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.00406

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.278

Alfa AF: 0.354 Hom.: 19138

Bravo AF: 0.251

Asia WGS AF: 0.112 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13073838; hg19: chr3-74627703;