rs4076052

Variant names:

• chr3-74492129-C-A
• rs4076052
• NM_020872.3:c.183-5498G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-74492129-C-A
• chr3-74492129-C-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.183-5498G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 152,230 control chromosomes in the GnomAD database, including 45 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 0.022 (45 hom., cov: 33)
• Consequence: CNTN3 NM_020872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 2 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=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN3	NM_020872.3	c.183-5498G>T		intron_variant	Intron 3 of 22	ENST00000263665.7	NP_065923.1
CNTN3	NM_001393376.1	c.183-5498G>T		intron_variant	Intron 3 of 22		NP_001380305.1
CNTN3	XM_011533768.3	c.183-5498G>T		intron_variant	Intron 2 of 21		XP_011532070.1
CNTN3	XM_017006508.2	c.8+883G>T		intron_variant	Intron 2 of 21		XP_016861997.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN3	ENST00000263665.7	c.183-5498G>T		intron_variant	Intron 3 of 22	1	NM_020872.3	ENSP00000263665.6

Frequencies

GnomAD3 genomes AF: 0.0221 AC: 3360 AN: 152112 Hom.: 44 Cov.: 33

Gnomad AFR AF: 0.00449

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0715

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0312

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0221 AC: 3367 AN: 152230 Hom.: 45 Cov.: 33 AF XY: 0.0221 AC XY: 1647 AN XY: 74436

African (AFR) AF: 0.00448 AC: 186 AN: 41544

American (AMR) AF: 0.0169 AC: 258 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3468

East Asian (EAS) AF: 0.0160 AC: 83 AN: 5176

South Asian (SAS) AF: 0.0714 AC: 344 AN: 4818

European-Finnish (FIN) AF: 0.0224 AC: 238 AN: 10608

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0312 AC: 2123 AN: 68004

Other (OTH) AF: 0.0251 AC: 53 AN: 2114

Alfa AF: 0.0191 Hom.: 16

Bravo AF: 0.0188

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.3
DANN	Benign	0.63
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism

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: rs4076052; hg19: chr3-74541280;