rs13073838

Variant names:

• chr3-74578552-T-C
• rs13073838
• NM_020872.3:c.-81+35839A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020872.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN3	NM_020872.3	MANE Select	c.-81+35839A>G		intron	N/A	NP_065923.1	Q9P232
	CNTN3	NM_001393376.1		c.-81+35196A>G		intron	N/A	NP_001380305.1	Q9P232

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN3	ENST00000263665.7	TSL:1 MANE Select	c.-81+35839A>G		intron	N/A	ENSP00000263665.6	Q9P232
	CNTN3	ENST00000962150.1		c.-81+35839A>G		intron	N/A	ENSP00000632209.1
	CNTN3	ENST00000962149.1		c.-81+35839A>G		intron	N/A	ENSP00000632208.1

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

African (AFR) AF: 0.104 AC: 4305 AN: 41526

American (AMR) AF: 0.241 AC: 3677 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1251 AN: 3468

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5176

South Asian (SAS) AF: 0.206 AC: 994 AN: 4824

European-Finnish (FIN) AF: 0.356 AC: 3765 AN: 10572

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25649 AN: 67784

Other (OTH) AF: 0.278 AC: 586 AN: 2106

Alfa AF: 0.335 Hom.: 30414

Bravo AF: 0.251

Asia WGS AF: 0.112 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.77
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13073838;

hg19: chr3-74627703;