chr3-3057490-A-G

Variant names:

• chr3-3057490-A-G
• rs17600202
• NM_175607.3:c.*1270A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175607.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN4	NM_175607.3	MANE Select	c.*1270A>G		3_prime_UTR	Exon 25 of 25	NP_783200.1
	CNTN4	NM_001206955.2		c.*1270A>G		3_prime_UTR	Exon 24 of 24	NP_001193884.1
	CNTN4	NM_001350095.2		c.*1270A>G		3_prime_UTR	Exon 25 of 25	NP_001337024.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN4	ENST00000418658.6	TSL:5 MANE Select	c.*1270A>G		3_prime_UTR	Exon 25 of 25	ENSP00000396010.1
	CNTN4	ENST00000484686.1	TSL:1	n.2601A>G		non_coding_transcript_exon	Exon 6 of 6
	CNTN4	ENST00000397461.5	TSL:5	c.*1270A>G		3_prime_UTR	Exon 24 of 24	ENSP00000380602.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.123 AC: 52 AN: 422

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.0491 AC: 2043 AN: 41568

American (AMR) AF: 0.124 AC: 1895 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3470

East Asian (EAS) AF: 0.00327 AC: 17 AN: 5192

South Asian (SAS) AF: 0.0413 AC: 199 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1630 AN: 10596

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.103 AC: 7037 AN: 68020

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0982 Hom.: 910

Bravo AF: 0.0861

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	9.3
DANN	Benign	0.83
PhyloP100		1.4
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: rs17600202; hg19: chr3-3099174;