rs17600202

chr3-3057490-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_175607.3(CNTN4):c.*1270A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 152,710 control chromosomes in the GnomAD database, including 753 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 0.089 (749 hom., cov: 33)
  • Exomes 𝑓: 0.12 (4 hom.)
• Consequence: CNTN4 NM_175607.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

Genes affected

CNTN4 (HGNC:2174): (contactin 4) This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

CNTN4-AS1 (HGNC:39985): (CNTN4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN4	NM_175607.3	c.*1270A>G		3_prime_UTR_variant	25/25	ENST00000418658.6
CNTN4-AS1	NR_046554.1	n.79+3577T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN4	ENST00000418658.6	c.*1270A>G		3_prime_UTR_variant	25/25	5	NM_175607.3	P1
CNTN4-AS1	ENST00000629672.1	n.446+1725T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0888 AC: 13507 AN: 152164 Hom.: 749 Cov.: 33

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0420

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0865

GnomAD4 exome AF: 0.121 AC: 52 AN: 428 Hom.: 4 Cov.: 0 AF XY: 0.109 AC XY: 28 AN XY: 258

Gnomad4 FIN exome AF: 0.123

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0888 AC: 13516 AN: 152282 Hom.: 749 Cov.: 33 AF XY: 0.0894 AC XY: 6659 AN XY: 74458

Gnomad4 AFR AF: 0.0491

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.00327

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0989 Hom.: 714

Bravo AF: 0.0861

Asia WGS AF: 0.0340 AC: 118 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	9.3
Dann	Benign	0.83

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: rs17600202; hg19: chr3-3099174;