3-74496626-T-C

Variant names:

• chr3-74496626-T-C
• rs6549604
• NM_020872.3:c.182+3033A>G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN3	NM_020872.3	c.182+3033A>G		intron_variant	Intron 3 of 22	ENST00000263665.7	NP_065923.1
CNTN3	NM_001393376.1	c.182+3033A>G		intron_variant	Intron 3 of 22		NP_001380305.1
CNTN3	XM_011533768.3	c.182+3033A>G		intron_variant	Intron 2 of 21		XP_011532070.1
CNTN3	XM_017006508.2	c.-43+3033A>G		intron_variant	Intron 1 of 21		XP_016861997.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN3	ENST00000263665.7	c.182+3033A>G		intron_variant	Intron 3 of 22	1	NM_020872.3	ENSP00000263665.6

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

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.799

Alfa AF: 0.883 Hom.: 78859

Bravo AF: 0.781

Asia WGS AF: 0.739 AC: 2571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs6549604; hg19: chr3-74545777;