rs4677400

Variant names:

• chr3-74479660-C-A
• rs4677400
• NM_020872.3:c.358+6796G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-74479660-C-A
• chr3-74479660-C-G
• chr3-74479660-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020872.3(CNTN3):​c.358+6796G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 152,040 control chromosomes in the GnomAD database, including 69,652 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 0.95 (69652 hom., cov: 29)
• Consequence: CNTN3 NM_020872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 0 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN3	NM_020872.3	c.358+6796G>T		intron_variant	Intron 4 of 22	ENST00000263665.7	NP_065923.1
CNTN3	NM_001393376.1	c.358+6796G>T		intron_variant	Intron 4 of 22		NP_001380305.1
CNTN3	XM_011533768.3	c.358+6796G>T		intron_variant	Intron 3 of 21		XP_011532070.1
CNTN3	XM_017006508.2	c.184+6796G>T		intron_variant	Intron 3 of 21		XP_016861997.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN3	ENST00000263665.7	c.358+6796G>T		intron_variant	Intron 4 of 22	1	NM_020872.3	ENSP00000263665.6

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145095 AN: 151922 Hom.: 69615 Cov.: 29

Gnomad AFR AF: 0.846

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.955 AC: 145190 AN: 152040 Hom.: 69652 Cov.: 29 AF XY: 0.956 AC XY: 71072 AN XY: 74310

African (AFR) AF: 0.845 AC: 35056 AN: 41462

American (AMR) AF: 0.981 AC: 14962 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3415 AN: 3466

East Asian (EAS) AF: 1.00 AC: 5144 AN: 5144

South Asian (SAS) AF: 0.999 AC: 4813 AN: 4816

European-Finnish (FIN) AF: 1.00 AC: 10610 AN: 10610

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67942 AN: 67980

Other (OTH) AF: 0.969 AC: 2045 AN: 2110

Alfa AF: 0.958 Hom.: 6375

Bravo AF: 0.949

Asia WGS AF: 0.992 AC: 3450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.35
PhyloP100		-1.5
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: rs4677400; hg19: chr3-74528811;