3-74496626-T-C

Variant names:

• chr3-74496626-T-C
• rs6549604
• NM_020872.3:c.182+3033A>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.182+3033A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,946 control chromosomes in the GnomAD database, including 50,038 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 0.80 (50038 hom., cov: 32)
• Consequence: CNTN3 NM_020872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.908 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.182+3033A>G		intron	N/A	NP_065923.1	Q9P232
	CNTN3	NM_001393376.1		c.182+3033A>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.182+3033A>G		intron	N/A	ENSP00000263665.6	Q9P232
	CNTN3	ENST00000962150.1		c.182+3033A>G		intron	N/A	ENSP00000632209.1
	CNTN3	ENST00000962149.1		c.182+3033A>G		intron	N/A	ENSP00000632208.1

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121236 AN: 151828 Hom.: 50030 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.798 AC: 121286 AN: 151946 Hom.: 50038 Cov.: 32 AF XY: 0.799 AC XY: 59318 AN XY: 74282

African (AFR) AF: 0.575 AC: 23811 AN: 41426

American (AMR) AF: 0.807 AC: 12295 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3047 AN: 3470

East Asian (EAS) AF: 0.722 AC: 3706 AN: 5136

South Asian (SAS) AF: 0.804 AC: 3878 AN: 4824

European-Finnish (FIN) AF: 0.914 AC: 9685 AN: 10598

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62079 AN: 67948

Other (OTH) AF: 0.799 AC: 1685 AN: 2108

Alfa AF: 0.872 Hom.: 97832

Bravo AF: 0.781

Asia WGS AF: 0.739 AC: 2571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6549604; hg19: chr3-74545777;