rs7518906

Positions:

• chr1-205075738-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005076.5(CNTN2):​c.*1973G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.82 (49132 hom., cov: 19)
  • Exomes 𝑓: 1.0 (10 hom.)
• Consequence: CNTN2 NM_005076.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

Genes affected

CNTN2 (HGNC:2172): (contactin 2) This gene encodes a member of the contactin family of proteins, part of the immunoglobulin superfamily of cell adhesion molecules. The encoded glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein plays a role in the proliferation, migration, and axon guidance of neurons of the developing cerebellum. A mutation in this gene may be associated with adult myoclonic epilepsy. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN2	NM_005076.5	c.*1973G>C		3_prime_UTR_variant	23/23	ENST00000331830.7	NP_005067.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN2	ENST00000331830.7	c.*1973G>C		3_prime_UTR_variant	23/23	1	NM_005076.5	ENSP00000330633	P1
CNTN2	ENST00000636312.2	c.*1860G>C		3_prime_UTR_variant	18/18	5		ENSP00000489754

Frequencies

GnomAD3 genomes AF: 0.821 AC: 118757 AN: 144630 Hom.: 49111 Cov.: 19

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.874

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.861

GnomAD4 exome AF: 1.00 AC: 20 AN: 20 Hom.: 10 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.821 AC: 118821 AN: 144730 Hom.: 49132 Cov.: 19 AF XY: 0.824 AC XY: 57816 AN XY: 70182

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.863

Alfa AF: 0.829 Hom.: 6548

Bravo AF: 0.808

Asia WGS AF: 0.932 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.51

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: rs7518906; hg19: chr1-205044866;