rs1374879

Variant names:

• chr3-74585946-T-C
• rs1374879
• NM_020872.3:c.-81+28445A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020872.3(CNTN3):​c.-81+28445A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,144 control chromosomes in the GnomAD database, including 1,195 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 (1195 hom., cov: 32)
• Consequence: CNTN3 NM_020872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN3	NM_020872.3	c.-81+28445A>G		intron_variant	Intron 1 of 22	ENST00000263665.7	NP_065923.1
CNTN3	NM_001393376.1	c.-81+27802A>G		intron_variant	Intron 1 of 22		NP_001380305.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN3	ENST00000263665.7	c.-81+28445A>G		intron_variant	Intron 1 of 22	1	NM_020872.3	ENSP00000263665.6

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17610 AN: 152024 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0878

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.116 AC: 17605 AN: 152144 Hom.: 1195 Cov.: 32 AF XY: 0.117 AC XY: 8681 AN XY: 74376

African (AFR) AF: 0.0536 AC: 2229 AN: 41558

American (AMR) AF: 0.163 AC: 2480 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1245 AN: 5150

South Asian (SAS) AF: 0.119 AC: 576 AN: 4822

European-Finnish (FIN) AF: 0.0878 AC: 930 AN: 10594

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9124 AN: 67980

Other (OTH) AF: 0.128 AC: 270 AN: 2110

Alfa AF: 0.125 Hom.: 633

Bravo AF: 0.120

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	14
DANN	Benign	0.65
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs1374879; hg19: chr3-74635097;